i've never repainted the heroclix figure, but i have tried some 1/72 plastics and had the paint flake of with use - as the plastic is so "bendy".
with that in mind, i would go with everyone else and advise to leave the original paint on as a binder and primer suited to that type of plastic. it seems better than going through the effort to strip and clean, paint ans then have your work flake right off.