If you wish to use the arrangement of textures you generated in Zbrush, you should then arrange your materials to match.

Alternatively, you can come up with a new arrangement of materials, load your update .obj into Zbrush and project (in Zbrush, this is part of the subtool menu) the materials and detail from your original model to the new .obj (you'll probably want to sub-divided it a few times.) To make sure Zbrush sees the new materials (and not the body parts), you'll need to set your zbrush preferences to "Import Mat as Groups" (this is under preferences -> import; by default it is set to "import polygroups", which is Zbrush's short hand for body parts in your model.)

Once your details and polycolors are projected to the new .obj. use Multi-map exporter to create a fresh set of maps matching the new arrangement of material zones.

I usually do a lot of projecting onto the final model after rigging to recover my detail and colors (and to do some touching up.)

-K

P.S. Here's a tut on reprojecting detail: https://vimeo.com/3213597