Your saves should be fine. Did you delete the Nintendo 3DS folder when you downgraded? There's no point in doing so.
If you already deleted it, complete your arm9loaderhax setup normally.
Afterwards, restore your NAND backup and copy back the backup Nintendo 3DS folder.
Dump your own encTitleKeys.bin using Decrypt9 (look up instructions on this), then reinstall your games that you own with freeShop (obtainable through FBI's TitleDB).
so they become playable again. If a game says that save data is corrupted, open the FBI program, go to Titles, find the game, and click Delete Secure Value. It should work now.