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Completely unrelated to the fangame, but if you change a Pokemon's species, evolve the newly changed mon, then change it again, the moveset will still be remembered. Tried it out by evolving Skitty, Igglybuff, Jigglypuff, then Cherubi. Igglybuff and Jigglypuff's moveset's didn't show up, but Skitty's and Cherubi's did, so I'd assume Igglybuff's moves were overwritten by Jigglypuff's, which was then replaced with Cherubi's.
Seems like SMD remembers two other mons' movesets for the move relearner, which makes sense, since a Pokemon only has two pre-evolved forms at max. This is probably used for recruitable evolved Pokemon like Flygon, who can only learn Earth Power as Trapinch.