ZBrush can’t handle multiple texture maps on a single model. As long as each map occupies a separate UV tile (so that, for example, one map has a UV space of 0,0, another is 0,1, etc.) then you can use the Multi Map Exporter plugin to output the separate maps from your polypainted merged model. If your model has UVs that occupy all the same UV space then output the maps (using Multi Map Exporter) before you merge the model.
After creating the separate texture maps for each subtool you can export all subtools as a single FBX file (using the FBX plugin) and that will probably load OK into C4D.