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It might be a "lost in rewrites" issue, since from the way they talk before the fix happens they do act like they've always had these cutie marks, but don't know why. That would be seen as Fake Memories to most (including whoever added that examples) but in context I do think the line was added so that "just restore their memories!" wasn't an easy solution. I'm still not sure how it counts either, maybe Ambiguous Situation? But I don't wanna jump to that right away, feels like a copout choice.
I would say it altered history if not for Ponyville only staring to going to hell the day after the switch as opposed to rewritten to already be screwed.
I asked the MLP forum
for their thoughts, but am asking here over the technical uses (like Fake Memories being fan speculations opposed to shown/stated).
I'll probably move this to Ambiguous Situation unless I hear otherwise.

My Little Pony: Friendship Is Magic S3 E13 "Magical Mystery Cure"
This seem explicitly contradicted by the episode as when Spike asks about using the memory spell to restore them Twilight states "It's not their memories, Spike. It's their true selves that have been altered!"
So due Fake Memories not apply if so directly contradicted? Still apply if it doesn't explain how this is different/more extensive than memory alteration? Or is Ambiguous Situation more fitting as it doesn't clearly explain how this worked?
And would Twilight's statement be Simple Solution Won't Work (an intended as legitimate explanation why not) or Hand Wave (a flimsy explanation self-aware about such), or is it/can it be both? I assume the former because it lack the attempt to deflect/dodge the issue.