In its non-overoxidized form, PPy (polypyrrole) is a conductive polymer. Once you start The overoxidation will transform the PPy electroactive film into a non conductive one. I have used the OPPy (overoxidized polypyrrole) as a non conductive permselctive membrane (see link), but for you case, i think you shouldnt do that. I dont think that MIP will work on OPPy. At least not in completely overoxidized PPy. But you can also control the degree of overoxidation, in case you need a partial overoxidation.
Over oxidation of pyrrole helps remove the inherent charge and can be used in molecularly imprinted polymer fabrication. My Question is does Overoxidation helps remove the template ? Yes to some extent or this process is enough to remove the imprinted template?