1. Backup emuNand with the emuNand tool.
2. Backup emuNand's files which are inside the Nintendo 3DS folder of your sd card.
3. Format emunand from system settings (normally)
4. On the newly formatted emuNand, set everything up again ( date, name, etc.) and link your NNID ( now you can).
5. Turn off 3ds. And restore the emuNAND backup and the folder you backupd previously.
6. DONE
It worked like charm, thanks so much.