hi.
maybe you can adjust the weights (each vertex), and delete the character in projectview, do not operate in winbrowser, then close the unity editor, recopy the new character to the folder..... ???
Similar problem.
A have 4 characters with the same skeleton. Two of them skinned in 3ds max with envelopes only, and two have custom vertex weights. All 4 works fine in unity. BUT! I need to change skinned mesh in prefab of one character to another. It works fine for characters with same skinning methods. But if I try to set a mesh with per-vertex skinning fo character with envelopes skinning - unity rotates part of the character breaking the skin.
I tried baking all vertex weights in 3ds max - it helps, but only in some cases.