I've seen many people ask how to do it, and I still can't imagine why anybody thinks it makes a difference, but the idea of how to do it just popped up in my head and it's really simple. You just have to go about it in a roundabout way.

1) Launch the GW menu and create a fresh NAND backup
2) Remove SD card and copy everything to your PC
3) Launch the GW menu again and format emunand
4) Reboot the system and format SYSNAND through system settings
5) Launch GW menu and make another NAND dump
6) Put SD card back in the computer and either rename the NAND.BIN that's on the SD card, or move it to a different folder than the original.
7) use emunand tool to inject this new NAND.bin onto the SD card
8) Copy all original SD card files, including the original NAND.bin back onto the SD card.
9) Replace SD card in 3DS and Launch the GW menu
10) Navigate to the downgrade function and hold UP on the D pad when you press A, to flash the original NAND.bin back.

You now have your original sysnand, with original files and progress on your SD card, while having an unlinked emunand. From there, you can follow other guides to update emunand to a version of your choosing.

Again... I still don't understand why anyone would think it needs to be done this way (perhaps because of GBA/DSi stuff, but PastaCFW+eshop spoof takes care of that (you can re-download after formatting sysnand)), but there you go.

 

[Deleted member 359653]

Couldn't you just do a system format while in emunand to unlink it?

 

[megazero1x1]

Couldn't you just do a system format while in emunand to unlink it?

But then let's say that you have a CIA installer on Emunand.
If you unlink by formatting it, then you also lose the CIA installer.

 

[MAXLEMPIRA]

Couldn't you just do a system format while in emunand to unlink it?

nowpe, if you Format emuNAND while linked, both sysNAND and emuNAND got Format, meaning a lost of games, saves, cia, etc.

 

[The Real Jdbye]

nowpe, if you Format emuNAND while linked, both sysNAND and emuNAND got Format, meaning a lost of games, saves, cia, etc.

Not if you backup your SD card first

 

[MAXLEMPIRA]

Not if you backup your SD card first

when you configure a new 3DS, it creates a new file on the SD, it's the same at the end...

 

[The Real Jdbye]

when you configure a new 3DS, it creates a new file on the SD, it's the same at the end...

If you format emuNAND, it will delete the files off the SD card but not format your sysNAND, so if you back up the files first you can restore them afterwards to keep all your stuff on sysNAND.

 

[MAXLEMPIRA]

Well, last time I tried to format emuNAND while linked with sysNAND, my 2DS format both sysNAND and emuNAND (fortunately I backup my sysNAND before). So, I don't know if nowadays isn't the same with new Gateway Firmware or rxTools

 

[Jhyrachy]

Thanks a lot!

I find this method really usefull because this way I can keep my sysnand clean from unsigned CIA so that even if I brick my emunand I will still be able to use my sysnand.

Maybe you can found it redundant, but I like to be safe!

 

[rewrewrew123]

Doesn't work for me. It says not enough space...damn!
I'm formatting SD and redoing from the beginning the procedure but I think that it will not work for me

 

[VerseHell]

Op why are you making this so complicated?
You just need to :
- Backup your sd card content.
- Format you console while in emunand. (Check if you can see GW3D first)
- Restore your sd card content.
That's all. (It's always nice to have a nand backup tough)

 

[metoob]

versehell, i tried this and i still only have one folder in the sd card. it didnt delete anything off the sd card.
EDIT: forgot to startup emunand. now i have 2 folders, but why didnt i have to back anything up?

 

[androgynus]

Hello, Sorry to superBump this thread, i just wanna know if anyone knows if this works on N3ds. I wanna keep my original SysNand and format emunand. Is what versehell said is right ?

 

[science]

Hello, Sorry to superBump this thread, i just wanna know if anyone knows if this works on N3ds. I wanna keep my original SysNand and format emunand. Is what versehell said is right ?

I would also like to have someone confirm this!

 

[kratoz29]

I don't get the difference between this method and others that I've seen here in other guides.

 

[Claod]

Hi, I got a problem and I'm not sure I can find the best solution....

I guess I need to unlink my emunand and nand to install custom themes on my emunand, but at this time I don't know what's good/bad by unlinking...

If I want to do it I need to format the emunand or the sysnand. During this process I'll need to turn Off the wifi, I'll need to use tinyformat (no need to put the SD card out, no problem with the NNID).
Emunand and sysNand will have differents directory with their own encryption key, so their datas will no longer be shared.


What is the best choice for me :
Should I format sysNand or Emunand in my case :

-I bought some appications on sysnand... if I format I'll still be in 9.2 ... I'll not be able to open the eshop to get my apps (pokebank and such, poketransfer etc ...) ... Any others risks ?
-In the emunand I have the same aplpications that in sysNand for now... And some extra CIA installed. So if I want to format to unlink I'll need to backup those saves / (is this possible for VC games?). Any others risks ?

I can't unlink and keep all my datas... except if I backup all my saves in emunand, format emunand with tinyformat and wifi off, reinstall all CIA, restore my saves... right? Is there any problems with NNID etc if I do so, please?

(PS: Sry to exhume this topic 1 year after the last reply)

 

[naivegirl2411]

Question... would this mean being able to keep my downloaded games and miiplaza/friendlist, etc data while also being able to run an unlinked emunand? Or is this data not saved in nand.bin?
Would this also work with decrypt9? If I understand this correctly this process involves formatting both emunand and sysnand to have both unlinked and clean and then flash your original nand.bin back?

 

[CarlangasLVDC]

Op why are you making this so complicated?
You just need to :
- Backup your sd card content.
- Format you console while in emunand. (Check if you can see GW3D first)
- Restore your sd card content.
That's all. (It's always nice to have a nand backup tough)

there're some saying that doing that formats both nands, could you verify that's not true, please?

 

[nakion]

there're some saying that doing that formats both nands, could you verify that's not true, please?

i just did it few hours ago on new 3ds xl 9.2.0 and it worked as it should sysnand is still intact only emunand got affected ! rly nice trick , btw on the new 3ds the wlan settings are shared no matter unlinked nands or not , idk why ;P not so dramatic