Ok I have seen a lot of confusion so I decided to make a guide on all the steps you need to take to go from higher than 4.5 firmware to lower than 4.5 with separated sysnand and emunand and eshop working normally. I won't go into detail on how every step is performed because there are already threads about them.

1) First you need to run the new Gateway Ultra 3.0.1b exploit and create a backup of your sysnand just to be safe. Keep this file on your PC

2) Then you go ahead and format emunand from gateway menu. (note that your sd card will be formatted so backup your data)

3) Then update your emunand via system menu while on gateway mode (CAREFUL WITH THIS STEP SO YOU DON'T UPDATE YOUR SYSNAND CAUSE IF YOU DO YOU CAN'T USE GATEWAY ANY MORE)

http://www.maxconsole.com/maxcon_forums/threads/286487-3DS-N3DS-Gateway-Ultra-Guide
This is the guide on how to come till here.

4) Now you are at a state that your sysnand and emunand share the same folder. You separate them by booting into sysnand, removing your SD card from 3ds and go to settings and format system memory. This will format your 3ds and erase anything (eshop games, NNID,etc,) but you already have them on emunand on the sd card. After formatting you will have to set up your 3ds again like if you run it for the first time. After setting it up again put your SD card back to your 3ds and let it configure on its own.

Benefits of separating sysnand from emunand is that you won't have to unwrap some of the apps you install every time you boot emunand, and settings like theme selection and folder/app arrangement will be unique on each nand and won't be affected by the other

5) Great now you have separated your sysnand from emunand but there is a problem. When you try to go into eshop from emunand you get an error. This happens because after format NNID info on sysnand are lost so you need to go back on sysnand and enter your existing NNID info on your 3ds. Do not create a new NNID. PUT EXISTING NNID ON SYSNAND NNID. After that you can get into eshop on emunand normally

6) Last step is to boot gateway mode, backup sysnand again and downgrade your 3ds via the gateway downgrade option. After doing so you end up with a 4.5fw sysnand (for EU 3ds, I don't know about US or Japan etc) and your emunand as you left it. Eshop works normally on your emunand and sysnand is separated from emunand.

Benefit of downgrading is that you don't need wifi any more to trigger the exploit. You just run the blue card once to install the exploit and then trigger it from system settings>profile settings>ds profile

 

[Liberty]

Best to tell you have to enter nnid in settings, NOT starting eshop (then you get a message of a new system update)

I didn't enter eShop at all and can't add the NNID on SysNAND. Just formated again to try. I always get a 022-2511 error telling me to update.

 

[kaiomar]

Ok I have seen a lot of confusion so I decided to make a guide on all the steps you need to take to go from higher than 4.5 firmware to lower than 4.5 with separated sysnand and emunand and eshop working normally. I won't go into detail on how every step is performed because there are already threads about them.

1) First you need to run the new Gateway Ultra 3.0.1b exploit and create a backup of your sysnand just to be safe. Keep this file on your PC

2) Then you go ahead and format emunand from gateway menu. (note that your sd card will be formatted so backup your data)

3) Then update your emunand via system menu while on gateway mode (CAREFUL WITH THIS STEP SO YOU DON'T UPDATE YOUR SYSNAND CAUSE IF YOU DO YOU CAN'T USE GATEWAY ANY MORE)

http://www.maxconsole.com/maxcon_forums/threads/286487-3DS-N3DS-Gateway-Ultra-Guide
This is the guide on how to come till here.

4) Now you are at a state that your sysnand and emunand share the same folder. You separate them by booting into sysnand, removing your SD card from 3ds and go to settings and format system memory. This will format your 3ds and erase anything (eshop games, NNID,etc,) but you already have them on emunand on the sd card. After formatting you will have to set up your 3ds again like if you run it for the first time. After setting it up again put your SD card back to your 3ds and let it configure on its own.

Benefits of separating sysnand from emunand is that you won't have to unwrap some of the apps you install every time you boot emunand, and settings like theme selection and folder/app arrangement will be unique on each nand and won't be affected by the other

5) Great now you have separated your sysnand from emunand but there is a problem. When you try to go into eshop from emunand you get an error. This happens because after format NNID info on sysnand are lost so you need to go back on sysnand and enter your existing NNID info on your 3ds. Do not create a new NNID. PUT EXISTING NNID ON SYSNAND NNID. After that you can get into eshop on emunand normally

6) Last step is to boot gateway mode, backup sysnand again and downgrade your 3ds via the gateway downgrade option. After doing so you end up with a 4.5fw sysnand (for EU 3ds, I don't know about US or Japan etc) and your emunand as you left it. Eshop works normally on your emunand and sysnand is separated from emunand.

Benefit of downgrading is that you don't need wifi any more to trigger the exploit. You just run the blue card once to install the exploit and then trigger it from system settings>profile settings>ds profile

Is this still working for latest version of GW ?

 

[Agent Moose]

So I know this thread is kinda old, but I do have a question:
When unlinking sys from emu, I understand that it creates another folder on your SD card so it can fully seperate the two.
Now, when I add my NNID back onto sysnamd after reformating it, will it be a different friend code?
Will my emunand NNID still have the old friend code, or will that also change?

 

[Lockheart456]

Don't know about this but there is no issue having internet connection on sysnand. Just don't let your 3ds go in sleep mode on sysnand and set your spotpass and send information options off on sysnand. There is no danger for update nag if you don't let 3ds go to sleep mode on sysnand.



Maybe if you don't have NNID you don't need to create one.

Is that safe to make NNID in GW mode? Or I just ignore NNID? because I think never create one once in 8.1 and now I in 4.2.

Notes:
I just have problem to buy apps, after all I still can connect eshop and download game update

 

[jimskeet2002]

I have NNID in GW mode without any issues