Let me quote this
You just have to make an emunand backup and a backup of your nand's folder in sdmc:/Nintendo 3DS/, then format emunand in system settings, re-link your NNID in your newly formatted emunand, then restore emunand backup and restore your folder in Nintendo 3DS so you don't lose your games and your saves.
use EmuNAND Tool (Google it its on here somewhere) to make the emunand backup
that's what i did.