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!
After I did system format in emunand, there are two folders in the SD:/Nintendo 3DS/ now,
but the subfolder in that two folders is the same value, like this,
/Nintendo 3DS/(hex1)/aabbccdd,
/Nintendo 3DS/(hex2)/aabbccdd,
Does It mean unlink nands failed?