On your 3DS run Decrypt9. Go to:
Code:
EmuNAND Options > EmuNAND Backup/Restore > NAND Backup > Select name.
When that's done, start over and go to
Code:
SysNAND Options > SysNAND Backup/Restore > NAND Restore (keep a9lh) > Select previously made emuNAND backup
When that's done, make sure to change your config on your CFW if needed.