Hello guys! I had the same issue of this thread:

Spoiler

https://gbatemp.net/threads/pairing-the-joy-con-on-emunand-and-sysnand.532494/

Practically, my joy-con and pro controller weren't synched anymore between EMUnand and SYSnand because I connected them to another console... so when I was switching from SYSnand to EMUnand (and vice versa) I had to redo the controllers pairing

In that thread, that's a way to re-sync the joy-con but you have to transfer a file from EMUnand to SYSnand and for me it's not very safe... So I found a way to transfer that file from SYSnand to EMUnand and keep the SYSnand clean!

So here is the tutorial:

WARNING:

SOMETIMES THIS TUTORIAL CAN LEAD TO THE "RED FIRST SETUP SCREEN" BUT DON'T PANIC! YOUR GAMES AND SAVES ARE SAFE, JUST COMPLETE THE SETUP AND EVERYTHING SHOULD BE AS BEFORE

WE FIGURED OUT THAT SOMETIMES THE SCRIPTS DOESN'T WORK PROPERLY WITH THE NEW HORIZONTAL MODE IF YOU HAVE YOUR JOYCONS ATTACHED SO IS PREFERABLE TO REMOVE JOYCONS BEFORE USING THE SCRIPTS.
I THINK THAT'S A TEGRA EXPLORER BUG AND NOT OUR'S.

I DON'T ASSUME ANY RESPONSIBILITY IF SOMETHING GOES WRONG SO PLEASE FOLLOW THESE STEPS ONLY IF YOU KNOW WHAT YOU ARE DOING

​

Preparation:
Download the latest version of Tegra Explorer from here: https://github.com/suchmememanyskill/TegraExplorer/releases
Download the right script according to your emunand type from the attached files (and make sure you choose it right)


ATMOSPHERE:

Spoiler

MAKE SURE YOU ARE IN AIRPLANE MODE ON EITHER SYSNAND AND EMUNAND, THIS PROCESS CAN "BREAK" YOUR DNS BECAUSE AS I KNOW, THE 8000000000000050 FILE CONTAINS ALSO WIFI AND OTHER SETTINGS AND THIS CAN LEAD TO BAN.
IF YOU'RE USING INCOGNITO MODE, YOU DON'T NEED TO BE IN AIRPLANE MODE. (BUT IS RACCOMANDED TO DO THAT)


1. Launch TegraExplorer.bin trough whatever you want (RCM loader, TegraRCM ecc…)


2. Go to [SD:/] SD CARD -> tegraeplorer -> syncfix -> Syncfix.te -> Launch Script
and follow the script instructions!

3. DONE!


If you pair your joy-cons/controllers to another console or you format your NAND (SYS or EMU), you have to launch again Syncfix.te to fix the sync issue!

SX OS EMUNAND AS HIDDEN PARTITION:

Spoiler

IF YOU'RE USING SXOS STEALTH MODE OR INCOGNITO MODE, YOU DON'T NEED TO BE IN AIRPLANE MODE.
ON THE CONTRARY, IF YOU ARE NOT USING THOSE, YOU HAVE TO BE IN AIRPLANE ON EITHER SYSNAND AND EMUNAND BEFORE PROCEDING.


DON'T USE TEGRAEXPLORER V2 OR LATER, INSTEAD USE THIS VERSION: https://github.com/suchmememanyskill/TegraExplorer/releases/tag/2.0.5

1. Launch TegraExplorer.bin trough whatever you want (RCM loader, TegraRCM ecc…)

2. Go to
[SD:/] SD CARD -> tegraeplorer -> syncfix -> Preparation.te -> Launch Script
and follow the script instructions!

3. REBOOT TO TEGRA EXPLORER

4. Go to
[SD:/] SD CARD -> tegraeplorer -> syncfix -> Syncfix.te -> Launch Script -> Launch Script
and follow the script instructions!

5. DONE!


You have to launch Preparation.te only the first time you follow this tutorial.
(Obviously, if you delete the emuMMC folder, you have to launch Preparation.te again but… dunno why you should delete it)

This script will create the following path on your micro sd:
sd:/emuMMC/emummc.ini
sd:/emuMMC/ER00/raw_based

This script is necessary to let Tegra Explorer read/write on your emunand and won’t affect it nowise.
If you pair your joy-cons/controllers to another console or you format your NAND (SYS or EMU), you have to launch again ONLY Syncfix.te to fix the sync issue!

SX OS EMUNAND AS FILE

Spoiler

IF YOU'RE USING SXOS STEALTH MODE OR INCOGNITO MODE, YOU DON'T NEED TO BE IN AIRPLANE MODE.
ON THE CONTRARY, IF YOU ARE NOT USING THOSE, YOU HAVE TO BE IN AIRPLANE ON EITHER SYSNAND AND EMUNAND BEFORE PROCEDING.
THIS SCRIPT IS TESTED ONLY ON FAT32 FILE SYSTEM, SO I DON’T KNOW IF IT WORKS ALSO ON EXFAT, LET ME KNOW IF THE EMUNAND CONFIGURATION IS DIFFERENT FOR EXFAT

DON'T USE TEGRAEXPLORER V2 OR LATER, INSTEAD USE THIS VERSION: https://github.com/suchmememanyskill/TegraExplorer/releases/tag/2.0.5

1. Launch TegraExplorer.bin trough whatever you want (RCM loader, TegraRCM ecc…)

2. Go to
[SD:/] SD CARD -> tegraeplorer -> syncfix -> Preparation.te -> Launch Script
and follow the script instructions!

3. REBOOT TO TEGRA EXPLORER

4. Go to
[SD:/] SD CARD -> tegraeplorer -> syncfix -> Syncfix.te -> Launch Script
and follow the script instructions!

5. DONE!


You have to launch Preparation.te every time you follow this tutorial.

This script will create the following paths on your micro sd:

sd:/emuMMC/emummc.ini
sd:/emuMMC/EF00/file_based
sd:/emuMMC/EF00/eMMC

Then, the script will move and rename all your Sxos emunand files from sd:/sxos/emunand/ to sd:/emuMMC/EF00/eMMC like this:

sd:/sxos/emunand/full.00.bin -> sd:/emuMMC/EF00/eMMC/00
.
.
.
sd:/sxos/emunand/full.07.bin -> sd:/emuMMC/EF00/eMMC/07
sd:/sxos/emunand/boot0.bin -> sd:/emuMMC/EF00/eMMC/boot0
sd:/sxos/emunand/boot1.bin -> sd:/emuMMC/EF00/eMMC/boot1


As I said, if you’re using exfat as your file system, please let me know if you have seven “full.XX.bin” files or less (or even more)!

This script is necessary to let Tegra Explorer read/write on your emunand.
As you can imagine, after launching Preparation.te, you aren’t able to boot to Sxos emunand, SO DON’T DO IT, just REBOOT TO TEGRA EXPLORER and launch Syncfix.te.
In Syncfix.te there’s a part that will revert the process so you can boot to Sxos Emunand again!

If you pair your joy-cons/controllers to another console or you format your NAND (SYS or EMU), you have to launch again FIRST Preparation.te, REBOOT TO TEGRA EXPLORER and THEN Syncfix.te to fix the sync issue!

Unfortunately, the Sxos version is still not running on tegragraexplorer v2 or later... so please, if you want to run the script safely on sxos, use this version of tegraexplorer until i'll update it to a newer version: https://github.com/suchmememanyskill/TegraExplorer/releases/tag/2.0.5

 

[Titan1907]

Hello thnx for ur time.
paired to the pc and tested the hardware; when pressing a button, the B value changes from 0.00 to 1.00.
all the buttons are tested and working.

 

[impeeza]

Hello thnx for ur time.
paired to the pc and tested the hardware; when pressing a button, the B value changes from 0.00 to 1.00.
all the buttons are tested and working.

Excellent so, we can says the joy-con is working fine.

yo can go to your console, with both joy-cons docked and select:

Settings -> Controllers and sensors -> Disconnect Controllers

You will be asked to press X to confirm, a message warning about you now can only use joy-cons is displayed and you should see two notifications about each of yours joy-cons being paired.

Now go to Settings -> Controllers and sensors -> Test Input Devices

And test each button of each joy-con, everything must work fine.

Undock each joy-con and test it again now using bluetooth communication.

 

[Kallim]

Hi. It's probably not quite the right thread but I'll try to help.

Unfortunately it sounds like your joycon rails. First try cleaning them.

Try a Friends joycon. If that also has issues you may need a new rail. They aren't hard to do if you can change thumbsticks etc. It depends how confident you are about opening it? Watch a video a few times before you try.

Last time I did one it was just the zif cable I basically took it out slightly (not even all the way) and reinserted it.... and it worked perfectly.

If it ends up being the joycon rather than the Switch you can also buy those rails. But try cleaning that too. You need to take the sl and sr buttons off to change that.

 

[Titan1907]

Hi guys thnx for the replies, problem solved..there was a problem with the ribbon cable connector..

 

[dcsilva29]

Hey everyone, I've tried using the script to sync my pro controller (my joycons were already synced) between both the sysnand and the emunand, but for some reason, even tho the script suposedly runs succesfully, it never actually syncs the controller, but seems to copy the wifi networks. At this point not even my joycons were synced. Even if i reattach and take them off they dont connect, unless i repair them trough the sync button.

I don't use atmosphere in my sysnand so the shared bluetooth database is not an option.
I'm using a mariko switch with a modchip, with the last version of atmosphere, HOS, hekate, tegraexplorer, etc. and I've tried two different variations of the same script here. the one linked in the first post and the one on post #98. My emunand is in partition mode.

I've disabled mission control to see if that changed anything but it didnt. Any idea what I might be doing wrong?

Is there any other way to manually replace the "8000000000000050" file in my emunand, other than using pc programs that change the emunand directly or edit a backup and restore?


edit: found the solution on post #177 (i dont know how to quote on an edit)
no clue how i missed it the first time, but in case in the future someone has the same problem, at least this will be on the last page/closer to it
may i suggest updating the script to delete the bluetooth_devices.db file? or notify the user to do so in case they encounter problems? i dont know anything about tegraexplorer scripts so i can't do it.

 

[impeeza]

today you can use Atmosphère Bluetooth Database emulation, so all emuMMC and SysNAND can share a only one Bluetooth database.

 

[dcsilva29]

today you can use Atmosphère Bluetooth Database emulation, so all emuMMC and SysNAND can share a only one Bluetooth database.

but for that dont i need to use atmosphere on both the sysnand and emunand? i'd like to keep the sysnand clear, and only run atmosphere on emunand

 

[Blythe93]

(i dont know how to quote on an edit)

I usually do select what I'd like to quote, click on Reply popup instead and it'll appear on a new post box. After that, I just cut and paste into a reply that I'd like to edit. Maybe not a proper way to do it, but that's how I do it.

but for that dont i need to use atmosphere on both the sysnand and emunand? i'd like to keep the sysnand clear, and only run atmosphere on emunand

@binkinator explained the whole sync feature between sysNAND and all emuNANDs here and here. I'm not sure if you need to run Atmosphere on both sysNAND and emuNAND, but maybe if you pair your controller on sysNAND it'll sync with emuNAND, haven't tested it myself so far as I'm mainly using emuNAND these days.