What future problems?
From this thread
http://gbatemp.net/threads/tutorial-installing-rxtools-custom-firmware-3ds-and-2ds.390867/
The benefits of unlinking your NANDs:
You will not have to unwrap all your games whenever you enter emuNAND.
This doesn't happen to everyone, but if it does, unlinking your NANDs will stop this from happening.
In the past, some users have reported their sysNAND updating even though they were sure they updated emuNAND. These same people happened to have linked NANDs. We don't know if it is related but it is safer unlink your NANDs if you fear this may happen to you.
You can go into sysNAND's Data Management (found in the System Settings app) safely.
Doing this while your NANDs are linked will result in your emuNAND games, saves, themes, etc. being deleted.
If you have Menuhax installed, you will not get a black screen when entering EmuNAND.
You can bypass this by holding a button when launching EmuNAND (which will disable Menuhax from loading). But who wants to remember to hold a button every time?
The disadvantages of unlinking your NANDs:
If you want to play GBA games in emuNAND, you will have to install the GBA game in both NANDs, taking up double the space.
If your NANDs are linked, you only need to install GBA games in sysNAND once.
Your sysNAND will be formatted.
Naturally, Devmenu2x will not be installed in Sysnand anymore, but it will be in EmuNAND. You can do Section 4 again if you want a CIA installer in Sysnand still.
Don't worry, everything that was on your sysNAND is in emuNAND instead.
If you don't like this, you can always use Decrypt9WIP or Gateway to restore your NAND.bin, thus recovering all your sysNAND stuff.
If you have Menuhax installed, it will be removed and you will have to reinstall it!
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Now the format isn't really a con as u won't be using it, gba games are small, and you just reinstall menuhax so that isn't really a con either. Having them linked can lead to more issue, just saying. Hell your having one of the issue now because they are linked and if you don't unlink you will still have the issue in the future