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Hmm, in terms of memory loss--I don't know how much this applies in real life, but in fiction it seems to tend to be about a person's identity, their social connections and personal history, right? Not so much their education/general knowledge, or other abilities; those are retained. I wasn't too sure about jumping to this conclusion since the Flask Plan does study abnormals, but it seems we can confirm now that Medaka will retain her abilities? In that case, I think this will simply provide an interesting reset of Medaka's character.
If we think about what makes Medaka 'Medaka', that important things are basically her past encounter with Kumagawa, and her osananajimi relationship with Zen. Medaka's relations with Akune and Kikaijima are fairly recent and not particularly involved on her part, and she wasn't especially fond of Maguro either--I think pretty much all Medaka's other relations aside from Zen could be recovered simply by telling her what they were in the past. As such, I think the primary effect of this development will be just those two things: first reverting Medaka back to her pre-Kumagawa state (introducing the possibility of bringing Kumagawa back into the story as well), and second presenting Zenkichi a challenge to their relationship that he may or may not want to accept.
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