it depends. the stuff on your sysnand (if you have any) will continue to be there since you'll backup up the files before formatting the SD card and you'll put it back afterwards. the stuff in emunand, only CIA saves might get affected but you can backup those too with savedatafiler. The other saves (.SAV) are in your SD card and like I said already, you're backing up your SD card's contents first
Just do it this way
1. Create backup of SD card.
2. Format SD card with SDFormatter.
3. Put stuff in SD card again (important so that sysnand doesn't think you lost your system folder)
4. Enter GW Menu and run Format Emunand.
5. Once Format Emunand is done, just power down the console. Do not enter the home menu.
6. Put back the files again inside the SD card since Formatting emunand only leaves the launcher.dat there.
7. Enter 3DS again and use it normally.
Btw... doing all this will only give you more trouble though. It will link back your emunand and sysnand again.
If you just restored your old NAND, configured NNID in sysnand and then downgraded again, you wouldn't have so much trouble.