hmm...... what are the chances there is a bondo with
flex agents in it? I've seen several people use just regular bondo on fiberglass with no problems, but I would think maybe if you mounted some mesh or something behind the holes and filled them with body filler it may do the trick.
The only other solutions I can think of is I have some tub and tile caulk/spackle which claims to have
flex agents and is paintable. I doubt however that this applies to automotive paints, nor could withstand the extreme temperatures that an auto environment would inflict.
but its a thought? hope this helps some!