Is prof Layton a NAND game? Does diskwriter say EEPROM-NO or EEPROM-YES for Prof Layton ROM?
After restoring, cycle PAST your game. Make sure it writes to the mSD.
You had the game working before, you backed up the savedata in Diskwriter, then you deleted. Then you WRITE same ROM back and RESTORE savedata backup. Still NEW GAME?
Hrm, here's a shot in the dark... before you made savedata backup in Diskwriter, did you press redbutton to go to next game BEFORE inserting mSD into PC? If not, savegame was never saved and you made an empty backup.
Try new game. When you make new game, get to savepoint. PRESS HOME>CLOSE>now press red button on Sky3DS. Light should blink then go to next game. Yes?
Now backup that game in Diskwriter. Delete old game. Exit Diskwriter. Start over. WRITE game, restore savedata backup, load on 3DS. Only NEW GAME? Or does game have SAVEGAMESLOT?
Understand?
You need to go to NEXT GAME BEFORE BACKING UP SAVEDATA IN DISKWRITER. Or savedata no exist when you do so.