Tutorial  Updated

How to have SEPARATE ATMOSPHERE AND SXOS EMUNAND HIDDEN PARTITIONS ON THE SAME SD TUTORIAL!

GOOD NEWS EVERYBODY!!! I have decided to make a..

How to have
SEPARATE ATMOSPHERE AND SXOS EMUNAND HIDDEN PARTITIONS ON THE SAME SD TUTORIAL!


PLEASE READ THE ENTIRE GUIDE BEFORE PROCEEDING. I WILL DO MY BEST TO MAKE THIS COMPLETE AND EASY TO FOLLOW.

I AM NOT RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS DUE TO THE USE OF THIS GUIDE. I DO THIS FOR FUN AND AM NOT A PROFESSIONAL. i HAVE TESTED THIS METHOD AND HAVE SET UP A COUPLE SD CARDS.

USE AT YOUR OWN RISK!!!!


The intent of this guide is to make ONE SD CARD with TWO HIDDEN EMUNANDS. One on 11.0 for SXOS and one with current firmware for Atmosphere.

More than likely the currently installed games WILL NOT WORK IN ATMOSPHERE if they were installed with the SXOS installer.

Tinfoil/awoo installed games may work fine. This is SXOS 's fault as the installer patched stuff in a way that is not compatible with the other CFWs.

There is also a section on SHRINKING the SXOS partition if you intend to only use it for USB loading. To minimize the impact it has on your SD and keep your HDD functionality for all 3000+ compatible games.. If you do this the current SXOS EmuNAND will break including installed games and saves.. IF you made backups of the save data you can restore them later.

Bottom line is, you will probably be reinstalling games and you need a backup of everything.

This guide make a few assumptions.. I will assume you are a current SXOS user with a working 11.0 Hidden Partition EmuNAND with a FAT32 SD. No Atmosphere installation required. There many ways to accomplish most things in this guide. I am doing the bulk of the work on the PC to limit the amount of times we take the SD out of the fragile Switch SD slot.

If you do not understand the above then this tutorial may be out of your league. Please google beginner switch hacking and learn some basics.

EmuNAND is the same thing as EmuMMC. It's just an older term. I call it by the old school term. Old habits..

This guide starts with a SXOS installation in place. If you wanted to go the other direction, adding a SXOS partition to an Atmosphere EmuNAND SD you would have to adjust accordingly but the main concept still stands.


DO NOT USE EXFAT!!! EVER! NINTENDO'S FAULTY DRIVER WILL CAUSE DATA LOSS!! DONT BE LAZY! FORMAT TO FAT32 AND DO IT RIGHT TO AVOID FUTURE ISSUES! I KNOW YOU DON'T WANT TO. DO IT ANYWAY! ANY EXPERIENCED PERSON WILL TELL YOU THE SAME. WHY WOULD WE ALL GO THROUGH THE HASSLE IF IT WASN'T NECESSARY? DO IT!



THERE ARE OTHER MULTI BOOT METHODS. THIS ONE IS THE MOST STABLE. YOU COULD JUST MAKE A FILE BASED EMUNAND FOR ATMOSPHERE. FILE BASED EMUNANDS ARE KNOWN TO CORRUPT. Good way to lose all your saves.

You will need a few things
  • Latest version of Hekate.
  • Latest NxNandManager
  • Latest EmuTool
  • Atmosphere SD files
  • Latest Sig Patches (the GBATemp thread)
  • A Raw Backup Of your SXOS EmuNAND (if you don't have one we will make one.)
  • A Backup of your current Atmosphere EmuNAND (if you don't have a current Atmosphere EmuNAND we will convert your SXOS EmuNAND)
  • A partition manager capable of moving and making partitions installed on your PC, I will be using MiniTool Partition Wizard but any capable partition manage should work.
  • A PC. Any should do, this guide is written with Windows in mind
  • A WORKING FOLDER ON YOUR COMPUTER (NxNandMnager and EmuTool can be quite finicky about external drives and things. Just make a new folder. For the sake of this tutorial I will use a folder CALLED C:\NANDS)
  • Keys.txt You can get these using Lockpick RCM or find them online.

BACK UP YOUR SAVES!!! I USE JKSV
BACK UP YOUR ENTIRE SD TO YOUR PC
This process will FORMAT YOUR SD!!!!!!


PREPARATIONS

Now we will set up the programs

On your PC:
  1. Make a folder for NXNandMananger. Folder can be anywhere except the working folder as long as you can find it.
  2. Unzip the NXNandManager .ZIP file to this folder
  3. Place the Keys.txt in the same directory as NXNandManager.
  4. Open NXNandManager, click OPTIONS then CONFIGURE KEYSET then IMPORT FROM FILE and point it to the Keys.txt.
  5. Unzip EmuTool and put the emutool.exe file anywhere except the Working folder as long as you can find it.

BACKUP CURRENT SXOS EMUNAND

If you have a raw backup already you may skip this step. Just put it in the working directory.
  1. Using a SD Reader insert SD with your SXOS EmuNAND in to computer.
  2. Run NxNandManager
  3. Select File > Open Drive> Select your SD.
  4. Select Full Dump
  5. Select Output Directory and choose your WORKING DIRECTORY. Name your backup. For the guide I name it SXOSemunandFULL
  6. Wait Until done
  7. Press OK
If you have a current Atmosphere EmuNAND you can back it up using the same steps now. Name it ATMOemunandFULL

OPTIONAL: Shrink SXOS EmuNAND

If you shrink your EmuNAND make sure you backup all saves first! Back them saves up even if you don't shrink the EmuNAND


If you would like to shrink your SXOS EmuNAND now is the time. This will make all installed NSP stop working. You can reinstall but it won't hold much. The intent is to make SXOS's impact minimal. I make SuperXCI (XCI files that contain all updates and DLC for the game) I convert NSP files and make Super XCIs out of them as well. This way Everything for SXOS compatible games is on the HDD. Except a Small EmuNAND.

You can select whatever USER data size you want. I only intend to have SAVE data on this EmuNAND so 8GB is enough for me. I play all NSP off of my SD in Atmosphere. SXOS is just for XCI USB loading.


In NxNandManager
  1. Select File>Open File and select your EmuNAND raw backup.
  2. Select Options > Resize EmuNAND
  3. Check Format User (this is optional, however this process will render the current USER data useless anyway so just format it to make it clean, Input file will not be altered)
  4. Select New Size.. I went with 5504 MB for user partition (8 GB Total) to keep enough room for saves.. some games have fairly large save files, you can choose whatever you want,
  5. Click Save As,, name the file whatever you want and choose the working directory. I call mine SXOSemuRESIZED
  6. Click Save.

Convert Hidden SXOS EmuNAND to Atmosphere File Based EmuNAND.

This will convert your Hidden Partition SXOS EmuNAND to Atmosphere EmuNAND files in the event that you don't have a Atmosphere EmuNAND backup. You should be able to migrate your saves and games over. GAMES INSTALLED USING THE BUILT IN SXOS INSTALLER WILL NOT WORK IN ATMOSPHERE.

If you have a raw backup from an Atmosphere Nand you can use that instead and skip this step. This section duplicates and converts your SXOS backup if you don't have an Atmosphere EmuNAND.
  1. Open EmuTool
  2. Under source select SXOS Hidden Partition
  3. Click "Select SD card" and select the SD with the SXOS Hidden Partition
  4. Under Select target select Atmosphere File.
  5. Under TARGET Click "Click to Select SD Card" Name the backup and save to the working directory. Ill Call it SX2ATMOemu
  6. Click START

Create New SXOS EmuNAND Partition

IF YOU ALREADY HAVE A SXOS EMUNAND IN A HIDDEN PARTITION ON THE TARGET SD YOU MAY SKIP THIS STEP
THIS SECTION WILL REFORMAT YOUR SD WITH THE NEW SHRUNKEN EMUNAND! YOU WILL LOSE ALL DATA!!! BACK UP THE SD FILES


In NxNandManager
  1. Select File > Open file and select the (Shrunken or not) backup of the SXOS EmuNAND
  2. Select Options > Emunand Creation Tool
  3. Check NAND path is pointing to your SXOS EmuNAND backup (Shrunken or not)
  4. Under "Select Emunand Type" Select SD partition
  5. Under "Select Target Disk" Select your target SD.
  6. Click "Create Emunand"


Resize FAT32 Partition and Make New Hidden Partition

THIS WILL MAKE ROOM FOR A SECOND HIDDEN PARTITION.



Now we will RESIZE your FAT32 Partition to leave a 29.2GB Unallocated Partition at the end of the SD
  1. Open MiniTool Partition Wizard
  2. Find the TARGET SD
  3. Right Click on the FAT32 partition
  4. Select Resize
  5. Reduce the size of the FAT32 Partition by 29.2GB using the slider. Make sure that the unllocated space AFTER the FAT32 partition is 29.2GB and DON'T MESS WITH THE UNALLOCATED SPACE BEFORE THE FAT32 PARTITION! THIS IS SXOS EMUNAND!!
  6. Press OK
  7. Right Click on the New Unallocated Partition after the FAT32 partition. (once again not the first one. That is your SXOS Partition.)
  8. Click CREATE
  9. In the "CREATE NEW PARTITION" window Select the following:
    1. Create As: PRIMARY
    2. Drive Letter: NONE
    3. File System: UNFORMATTED
    4. Cluster Size:; NONE
    5. Click OK
  10. In the MAIN WINDOW press Apply
That should format the unallocated space so the tools can see it.

Make new Atmosphere Hidden Partition EmuNAND

In EmuTool
  1. Under "Select source" select Atmosphere files (Or hekate back up files if that's what you have)
  2. Select "Click to select SD Card" and point to the Converted SXOS to Atmosphere Backup files (SX2ATMOemu) or your Atmosphere Backup, You must point to the directory with the BOOT1 BOOT2 00,01 etc etc files, Probably emummc\(A Numeric Code)\eMMC\
  3. Under "Select Target" Select Atmosphere Hidden partition
  4. Select "Click to select SD card" and point to your Target SD card.
  5. Press START.
Restore SD backup and install Atmosphere
If all went well you should be able to copy your SD files you backed up in the beginning of the guide. That should get SXOS back up and running. then you can install Atmosphere. There are a TON of guides. just get the newest SDfiles and toss them on the SD. You'll need sigpatches too if you want to play downloaded content.

  1. Copy FILES YOU BACKED UP IN THE BEGINNING OF THE GUIDE back to the SD FAT32 Partition .
  2. Copy all Atmosphere files to your SD
  3. Copy Sigpatches to the SD
If you are converted your EmuNAND from SXOS to Atmosphere and you didn't shrink your EmuNAND you need to copy the files in the EMUTENDO folder contents from SXOS to the Atmosphere NINTENDO folder (emuMMC/XXXX/Nintendo, XXXX is a Alpha Numeric 4 digit ID) this should make everything compatible work.
(Remember games installed with the built in SXOS installer will probably need to be reinstalled.)

Make EmuNAND visible to Atmosphere.

  1. Unzip Hekate files to the ROOT of your SD.
  2. Insert SD in to the Switch
  3. Boot Hekate using the hekate payload and your favorite payload launching method.
  4. Select EmuMMC
  5. Select Migrate EmuMMC
  6. Select Fix Raw
  7. Select OK
Now you should be able to boot in to SXOS and Atmosphere each with their own EmuNANDS!!! Just boot the payload for the CFW you want using your favorite injection method.

Now you can update the firmware for your Atmosphere EmuNAND using daybreak. There are MANY guides on the subject. Google it!

Make sure your games work. Then you can uninstall duplicate games from the SXOS. You can move games from SD to System NAND in the Switch Data management Menu while in EmuNAND. This will move them from the FAT32 partition to the Hidden EmuNAND to free up the FAT32 even more. Remember to leave room for save files.


EXTRAS!

Here I would like to make a few suggestions....

TESLA with the FastCFWSwtich overlay,

If you would like a convenient way to switch between the CFWs (and other things too) I recommend you install TESLA with the FastCFWswitch overlay. Once installed you can Hold down L and DPad Down then Click the right joy stick to bring up Tesla at any time. It allows you to run "overlays" that are basically just homebrew programs. Emuiibo is a great Amiibo emulator, there is a fast reboot, a UMS feature, FTP etc. in this case I recommend FastCFWswitch.

FastCFWswitch allows you to switch between different CFWs with a few clicks.

TESLA page on GBATemp
This is the page for Tesla. In this instance the trick is to install it for BOTH SXOS AND ATMOSPHERE.

  1. Download the latest fastCFWswitch NX-ovlloader and Tesla-Menu
  2. Unzip all to the root of the SD
  3. You must manually copy all the \atmosphere\contents files from NX-ovloader zip file to SXOS\titles\ to make it work in SXOS too, (I will make a pack if the developer gives me the green light.)
That's it. in SXOS or Atmosphere you can press the hotkey combo.. (hold down L and DPad Down and Click the right joy stick) to bring up the TESLA menu, then select fastCFWswitch and the CFW you want and off you go.

I suggest using different themes on your EmuNANDs so that you can tell them apart at a glance. There are SXOS and Atmosphere versions of my skeletal themes,

Skeletal Switch Theme
Skeletal TV theme
Skeletal HDD for SXOS Theme <-- Made this today

I will add more stuff and tweak this out as I have time. Please feel free to ask questions. It will help me fine tune this tutorial.

CHEERS!

Thanks to Maupiti for all the help.:grog::grog::grog::grog::toot::toot::toot::D
 
Last edited by mikefor20,

Blythe93

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You need to add an entry to Hekate to make it boot sx
Thanks for the example. ^^ It doesn't seem all that complicated.
As far as your remote sync, did you format the emunand? that changes a descriptor and "Separates them". I will figure out how to to fix it. Stays synced for me.
I didn't format the emuNAND, I think. But I did connect my joycons to my OLED Switch so that's most likely the reason. I hope you'll find a fix for it, fingers crossed!
 

Xsaber

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You should be able to create an unformatted area before the FAT32 partiton by shrinking the FAT32 partition and try put a SXOS emuNAND there with EmuTool. Source SXOS files (point to your SXOS file based EmuNAND) Target SXOS hidden partition . Least amount of work that way I think. I am not sure though as I have not tried it and SXOS might need something more to see it. similar to the migrate emummc step. I dont know of any tools to do this. IDK. If you try this let me know and I will add it to the main guide.

Or you could back up the Atmosphere hidden partition and use that backup and the SXOS file based EmuNAND files following the guide. Make backups with EmuTOOL. Use the atmo backup during the Make new Atmosphere Hidden Partition EmuNAND section and the SXOS files during the Create New SXOS EmuNAND Partition Section. I am 99% sure that would work. Just haven't tried it.

Please let me know what you did!
sorry to necropost this thread, but i was wondering if you might potentially be willing to help me with a problem I'm having?

so I have a modchipped oled that iv'e set up with hekate running atmosphere. set it up with the HATS package. my issue that i'm having is i want my sysnand to run a different atmosphere than my emmunand. mostly so that I can keep them separated completely. I use the sysnand for editing saves.

I've set it up so that emmunand is completely blocked off of Nintendo's servers with exosphere.ini altering prodinfo for it, as well and blocking all of Nintendos servers for the emmunand cfw specifically. the issue I've run into is when I install themes and other apps from the Homebrew menu they show in my sysnand cfw due to being a part of the same atmosphere.

so that leads me to my question. i would like to set hekate up to dual boot atmospheres so that emmunand is isolated in its own sandbox able to use cfw without affeecting sysnand cfws homebrew. iv'e thoroughly researched for hours on how to do it but I havn't found much that would suggest anyone else has done it. unless I'm just making it too complicated. in which case please enlighten me on how to make it so that my emunand is separated on its own atmosphere that doesn't affect any files on my sysnand cfw atmosphere.

Edit: the only thing im seeing online that would potentially do it is dual booting atmosphere with another custom firmware like SXOS. however im relatively new to the modding scene with the switch. i feel like that would work, but id rather be sure before spendind a large amount of time trying it only to find out emunand homebrew isnt isolated to emunand...

I'm probably making it too complicated. so if you have anything that will help I will be more than grateful :)
 
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OldGnashburg

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Can you make a tutorial for a sd partitioned with Hekate, I created 2 EmuNAND partitions as well as a linux and android partition and EmuTool is not working the way I want it.

Edit: Managed to format things they I need to but still not working. I've been trying forever to get a 1TB sd working with Android, Linux, Lakka, SXOS Partition, Atmosphere Partition? How do I do this? This is frustrating.
 
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mikefor20

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sorry to necropost this thread, but i was wondering if you might potentially be willing to help me with a problem I'm having?

so I have a modchipped oled that iv'e set up with hekate running atmosphere. set it up with the HATS package. my issue that i'm having is i want my sysnand to run a different atmosphere than my emmunand. mostly so that I can keep them separated completely. I use the sysnand for editing saves.

I've set it up so that emmunand is completely blocked off of Nintendo's servers with exosphere.ini altering prodinfo for it, as well and blocking all of Nintendos servers for the emmunand cfw specifically. the issue I've run into is when I install themes and other apps from the Homebrew menu they show in my sysnand cfw due to being a part of the same atmosphere.

so that leads me to my question. i would like to set hekate up to dual boot atmospheres so that emmunand is isolated in its own sandbox able to use cfw without affeecting sysnand cfws homebrew. iv'e thoroughly researched for hours on how to do it but I havn't found much that would suggest anyone else has done it. unless I'm just making it too complicated. in which case please enlighten me on how to make it so that my emunand is separated on its own atmosphere that doesn't affect any files on my sysnand cfw atmosphere.

Edit: the only thing im seeing online that would potentially do it is dual booting atmosphere with another custom firmware like SXOS. however im relatively new to the modding scene with the switch. i feel like that would work, but id rather be sure before spendind a large amount of time trying it only to find out emunand homebrew isnt isolated to emunand...

I'm probably making it too complicated. so if you have anything that will help I will be more than grateful :)
Unless you did something weird,each atmosphere EmuNAND has its own folder. It's always seperate unless you tweak the ini. That's the whole point. What happens in emunand stays in EmuNAND.
Can you make a tutorial for a sd partitioned with Hekate, I created 2 EmuNAND partitions as well as a linux and android partition and EmuTool is not working the way I want it.

Edit: Managed to format things they I need to but still not working. I've been trying forever to get a 1TB sd working with Android, Linux, Lakka, SXOS Partition, Atmosphere Partition? How do I do this? This is frustrating.
There is a Quad Boot tutorial already. Did you try that? IIRC the SX and Switchroot partition occupies the same space so you use Hekate to build Fat32, Switch root, linux and Atmo partitions then use a file based one for SX. When I have time I'll look at it.

Thanks for the example. ^^ It doesn't seem all that complicated.

I didn't format the emuNAND, I think. But I did connect my joycons to my OLED Switch so that's most likely the reason. I hope you'll find a fix for it, fingers crossed!
My joycons sync fine between Atmo and sx. Tried them on my OLED too. No problem. Idk what to say..
 

Blythe93

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My joycons sync fine between Atmo and sx. Tried them on my OLED too. No problem. Idk what to say..
I see... How would you go about adding new joycon pair to your Switch? I know how to sync them between sysNAND and Atmos emuNAND (there's a script for that that works), but what about SXOS emuNAND (there's one for SXOS as well, but for some reason it doesn't work, I've posted the error I run into here)?
 

mikefor20

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I see... How would you go about adding new joycon pair to your Switch? I know how to sync them between sysNAND and Atmos emuNAND (there's a script for that that works), but what about SXOS emuNAND (there's one for SXOS as well, but for some reason it doesn't work, I've posted the error I run into here)?

I am not sure your nands are linked.
There's a descriptor, (console ID I think. Maybe...) Formatting changes it. I am not sure if Emutool changes it. I doubt it or everyone would be having issues. The tutorial was written to be easy and limit removal of the SD. There are a lot of variables though. You could be converting SX to Atmo, making a new atmo emunand. Maybe your Sysnand was formatted since the first EmuNAND was created.

If you started with a clean switch, made a SX emunand and then converted to Atmo they all be synced. To add after just means syncing agin since the descriptor hasnt been altered.

There's a sys check homebrew.. sysid? Im not home. Run it in all 3 nands and see if everything is the same. Incognito can check too. Tinfoil too. In think they're separated so when you sync to one it desyncs the other. Im not sure exactly what you did. Also that script is not something I'm familiar.
 
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Blythe93

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I am not sure your nands are linked.
It could be that I did something along the that changed its descriptors as you call them. I'm not really familiar with terms, sadly, but I will check for that tool you mentioned and reply back as soon as possible.
If you started with a clean switch, made a SX emunand and then converted to Atmo they all be synced. To add after just means syncing agin since the descriptor hasnt been altered.
That's how I went (unless I made a not-so-obvious mistake). I posted here how I got my SX OS emuNAND to work and after that I followed your guide step by step. Now that i think about it, could it be that its descriptor didn't carry over because of the failed USER partition restore when I downgraded my SX OS using downgraded Atmosphere emuNAND backup as a base?
 

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Hi, I have a dual boot setup (Atmosphere and SXOS both on hidden partition emuNANDs) but I can't seem to launch SXOS directly from Hekate anymore, it used to work just fine when I first set this up like a year ago, now, all I am getting is either a black screen or an missing Boot.dat message.
Below is the SXOS entry in my hekate_ipl.ini file:

Code:
[SX OS (emuNAND)]
payload=Bootloader/payloads/SXOS.bin
icon=Bootloader/res/icon_sxos.bmp
id=sxos

is there something I am missing here? Switching between Atmosphere and SXOS is fine when using fastCFWswitch.
 

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Hi, I have a dual boot setup (Atmosphere and SXOS both on hidden partition emuNANDs) but I can't seem to launch SXOS directly from Hekate anymore, it used to work just fine when I first set this up like a year ago, now, all I am getting is either a black screen or an missing Boot.dat message.
Below is the SXOS entry in my hekate_ipl.ini file:

Code:
[SX OS (emuNAND)]
payload=Bootloader/payloads/SXOS.bin
icon=Bootloader/res/icon_sxos.bmp
id=sxos

is there something I am missing here? Switching between Atmosphere and SXOS is fine when using fastCFWswitch.

I had this problem before, you can use Argon to boot into SX OS and Hekate then boot into Atmosphere if you are doing dual boot.
 

Maupiti

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Hi, I have a dual boot setup (Atmosphere and SXOS both on hidden partition emuNANDs) but I can't seem to launch SXOS directly from Hekate anymore, it used to work just fine when I first set this up like a year ago, now, all I am getting is either a black screen or an missing Boot.dat message.
Below is the SXOS entry in my hekate_ipl.ini file:

Code:
[SX OS (emuNAND)]
payload=Bootloader/payloads/SXOS.bin
icon=Bootloader/res/icon_sxos.bmp
id=sxos

is there something I am missing here? Switching between Atmosphere and SXOS is fine when using fastCFWswitch.
Could be the latest version of Hekate related if you’re on latest.
I would suggest as @Hayato213 said.
My dual boot works fine, but I’m very far away from being “updated “…🤣

But in any case using my RCM Loader I have multiple direct entries
 
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eChorza

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Could be the latest version of Hekate related if you’re on latest.
I would suggest as @Hayato213 said.
My dual boot works fine, but I’m very far away from being “updated “…🤣
I have an internal SAMD21 chip (Rebug SwitchME, 6 wire install), I ended up using Payload1.bin (SXOS) as the main payload after disabling Payload.bin (Hekate) in the chip settings. Now, my Switch autoboots to SXOS and from there I can boot to Hekate or Atmosphere directly via fastCFWswitch.
 
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Maupiti

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I’m on V1 unpatched, no chip. AutoRcm, so everything sd card related.

I love FastCFWswitch , one of the best overlay .
 

Hayato213

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I have an internal SAMD21 chip (Rebug SwitchME, 6 wire install), I ended up using Payload1.bin (SXOS) as the main payload after disabling Payload.bin (Hekate) in the chip settings. Now, my Switch autoboots to SXOS and from there I can boot to Hekate or Atmosphere directly via fastCFWswitch.

Funny thing I think it might be the trinket as I have a trinket M0.
 

Maupiti

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Hekate boot fine, like @eChorza said sometime it won't boot SX OS with hekate.
Humm. strange…🤔

I used a trinket M0 that I modded but on external dongle. Never used internal.
Never had issues .
Previously on Sxos dongle that died 🙄

Now very happy with my RCM Loader One that have lots of entries.
 
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eChorza

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Humm. strange…🤔

I used a trinket M0 that I modded but on external dongle. Never used internal.
Never had issues .
Previously on Sxos dongle that died 🙄

Now very happy with my RCM Loader One that have lots of entries.
I am really having a headache for the last day or so.

I am using an internal SAMD21 chip, my Switch is setup with EmuNAND for SXOS and emuMMC for Atmosphere.
The trouble I am having is loading anything from USB on SXOS, I tried using a flashdrive directly connected to the Switch USB-C port and also a powered USB HDD connected to the dock and also tried it connected to the Switch directly.

In all scenarios, I can load the games but 5-10 seconds later, the console freezes completely and I have to hold the power button down to turn it off.

Does anyone know what the issue might be? I was wondering if the SAMD21 chip is maybe using the USB data lines and conflicting with the whatever is connected there? I flashed my chip (Rebug) using @mattytrog Fusee_Suite UF2 packages.
 

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