1) What happened
PrefabUtility.CreatePrefab does not copy the whole game object when used in OnPostprocessModel.  Mainly, you can look at the mesh on the skinnedmeshrenderer, and it will be null.

2) How can we reproduce it using the example you attached
I provided a 3D maya file.  Copy the file somewhere outside of Unity, then delete the reference in Unity.  Then drag the model back into Unity.  Look at the prefab that was created.  In the CenterRoot, there is a SkinnedMeshRenderer, and the Mesh does not contain a reference.  However, if you drag the mesh straight to the scene, it contains the proper reference.  On top of that, this only happens in the OnPostprocessModel, not in a normal function.

This will also make all the animation clips null, but an example is not provided in the project.

This is very critical to my project, and I have not found a work around.  Please, at least let me know that this will be worked on and attempted to be fixed soon.