I don't think I would let him touch them again. Maybe you can send them to a recommended cobbler and let them do their best to fix the nicks and ask if the soles can be redone at all.
This.
And as for what will happen if the rubber is removed, here's what my shoes looked like and this was after I sanded the hell out of them in attempt to smooth them out (and painted over with red paint).
Frankly, I would rather have the higher rubber than have them look like that.