My guess is that if time and pressure did that, time and pressure will remedy that... Try to get foam inside the tires, and put some extra foam on the inner side of the flat spot, thus creating a small protruding bump. Leave it like that a couple of weeks, maybe a month, I think that would cure them.
I always leave all my cars "jacklifted" when they are not in use to avoid this. Spare tires also always keep them resting flat.
Good luck!!
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