Success!

Special thanks to goast666 on the ZBrush Central forums for helping out with the import workaround.

The Problem: ...was happening not on export from ZBrush or even import on ZBrush, but importing directly into an existing subtool level to update the UV's with UV's laid out in an external app (in this case Maya).

The Solution:
1. "Store" a "Morph Target" on the subtool layer before you import the new OBJ.
2. Import the OBJ. At this point the scale and position will be totally off.
3. Hit the "Switch" button in the morph target UI to snap the newly imported OBJ into the correct position and scale.
4. Then "Delete MT" (delete the morph target) for a quick clean up.

Worked like a charm and kept all the new UV's intact.

Thanks again goast.

More Problems...

This lovely image is what's happening to my Zbrush tool when I simply export each subtool out to a OBJ then import them right back in to the same position in the tool. As you can see, the scaling and position of the subtools goes out the window on import.

The export looks sound since I can import the OBJs into Maya and everything looks super.

In fact, after just doing a simply test in Zbrush....importing the individual subtools into ZBrush and the assembling them back into one tool ends up with great results. But that doesn't get the details and the color back onto the newly imported subtools.

Still working on this one....but I'm running out of duct tape.