Pokemon Mystery Dungeon: Explorers of Sky Help

There is something wrong with the game. All the pokemon except store pokemon are gone. I think it has something to do with the cheats. I have tried turning them off, but the pokemon are still not there. I have beaten the main part of the game. Does anyone else get this problem?

The negative effects of cheat codes on a save-file are usually irreversible unfortunately. It's advisable to backup your save-file if you have made decent progress in-game before enabling cheats.