If I do format system memory in emunand instead, will it also unlink sysnand and emunand?
Thanks.
Yes. Format with no SD card in though
Formatting emunand instead of sysnand will unlink the nands just fine.
Be sure to back up the folders within :/SDCARD/Nintendo 3ds/ and to restore them afterwards. After you've formatted and restored it, the folder you should have 3 subfolders (the original hexadeximal, the new hexadecimal for the freshly formatted emunand and a Private folder)
Good luck!
I'm not entirely sure. The ones i have in my backup are different to eachother, but that may be due to my system transfer. There's an easy way to check though, do the emunand and sysnand have a different friendcodes? If so, they're unlinked.