You never unlinked your NNID from Sysnand before setting everything up do this
1) Backup emunand and backup its folder in sdmc:/Nintendo 3DS/ (easier method: add a _ or something at the end of the folder so you don't have to copy it off your SD card, OR cut/paste it to the root of your SD card)
2) Go in emunand system settings, pick system format
3) Let it do its thing
4) Log into your NNID on newly formatted emunand
5) Restore emunand backup and put its folder back in sdmc:/Nintendo 3DS/
Use this to backup your Emunand
https://gbatemp.net/threads/emunand-tool-release-and-support-thread.359239/