I think HitmonInfinity is right... So as a test, I made a cube and deleted all the default UVs. I mapped 5 faces onto map1, the default UV set. I create a new UV set and then map the last face into this new UV set. I select the UVs of the lone face in the new UV set and then copy it to map1. I switch back to Map1 and it…
As JMYoung did, I was using Copy UVs to UV Set, and also tested in Maya 2011 64-bit. Is this still not doing what you needed? Anyway, I'm not sure what combining meshes or extracting faces has to do with fixing UV sets, but if that is getting you the results you're looking for then you could copy the skin weights from the…