Issue

You export a skinned model to Fbx an file then import it back into a new Maya scene as Fbx, then all the skin clusters skin weights are corrupted, and don't match the skin weights from the original scene file. If you investigate deeper, you may even notice Maya is recreating all skinclusters from scratch while importing the Fbx file 😵

Sometimes your scene gets corrupted, so exporting to Fbx results into a corrupted Fbx file. When importing back the file into Maya, it will attempt to fix the issues which may explain this weird behavior.

Things to look for

• Check error logs when importing / exporting C:\Users\%username%\Documents\maya\FBX\Logs and fix it.
• Maybe your bind pose nodes are corrupted? Attempt to reset bind pose node. You can also reset the bind pose information at the skincluster level as well with this script.
• Sometimes there are no errors: in my case a few joints had duplicated .matrix connection to the skincluster, so check the skincluster node is setup with the correct connections and parameter. (Does the paint tool works properly on that rig, if not chances the skincluster setup is corrupted.)