What you need to do is find a quest where you have the same amount of units as the one where you used the cheats. Once in a quest, move the characters and select separate. Hope this helps.
@Xdqwerty, Osu! Tatakae! Ouendan! is the Japanese version of the game, different settings/characters/songs but otherwise identical mechanics. I played that before I knew about Elite Beat Agents lol. Both fantastic games https://en.wikipedia.org/wiki/Osu!_Tatakae!_Ouendan