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I assume that once the procedure was completed (fairly invasively, judging by the scars on her chest), Chise was able to regenerate the damage caused by the surgery. After all, after battles she was able to change the shape of her limbs back to normal. So it's not illogical that she could be back at school the next day.
The OVAs make it clear that the military has tried the procedure on other people before. (However, it could very well be that there is something about Chise in particular that made her more suitable for being turned into an ultimate weapon.)
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