Replacing skinned mesh prefab problem

Hey, I am having some kind of issue with my prefabs when I reimport a skinned mesh. I replace the file by overwriting the old .fbx with a new version, and it imports just fine, even if I look at the imported mesh in unity it's fine.

However, all my prefabs that use that skinned mesh have gotten weird issues (it seems kind of random what happens to it, depending on what I change), like sometimes the mesh is welded to the bones and makes it look like a stick person, other times just one part of the mesh will freak out, and again, this is only effecting the prefabs. Reverting on the prefabs don't work either, as it's broken as soon as an original prefab is placed.

So I'm wondering if there's a more reliable way to import a mesh, refresh the prefabs, or at least something I can do to have the prefabs not freak out? Since the import isn't broken I could go around and replace each and every one and it would work fine, but that takes quite awhile with how many prefabs I have.

If it's helpful: My Skinned Mesh .fbx has 13 mesh parts, one animation, and isn't compressed. My prefabs are simply the skinned mesh with a few scripts on them that are not executed in the editor and sometimes an attached weapon mesh into the hands.