first of all…UV has nothing to do with UV maps !! why u doubt ! b’se skinWeight is like a percentage of influence weights of bones per vertex.
its like … ok, for vertex 1 - joint 1 will weight it by 40 and joint 2 by 60 % and for vertex 2 - joint 1 by 55 % and joint 2 by 45 %… and so on… thats it, nothing else !!
UV comes into play ONLY if u want to use maya’s default export skin weights tool… when u fire this, maya looks at the UV map and for each joint in the skin cluster, exports an image out…
ok, since this is clear now, i wud also suggest this :
dup ur skinned mesh, UV what u want on this. since ur mesh is a ‘deformed’ object, select it , go to deform menu > show intermediate object (this is the orig model copy maya uses to compare to find out resulting deformations - pls correct me if i’m wrong) and then u can select ur dup mesh (with new uv on it) and select this intermediate object, try UV transfer tool… then if u want to remove even this node (to keep lesser history), <read carefully> select the intermediate shape node, in hypergraph, only disconnect the incoming connections from the polyTransfer node to the shape node… and then delete the polyTransfer node… this way ur uv is put no the shape and the history is gone !
this way u can avoid the skin weights xport and import but if u want to do this, yes i suggest usign a tool like arcsecond suggested… non-UV dependent export tool…
hope that helps !