Boot into Hourglass9. How were you planning to restore a NAND backup using FBI?
Edit: oops misread the question! If your home menu doesn't work then there's not a lot you can do. You can try updating it, if not on 11.3 yet. If that doesn't work then you'll have to restore your backup.
Also, remember that your games and saves are in the Nintendo 3DS folder. The only thing you'll lose by restoring an old NAND backup is Activity Log, Mii Plaza etc.