Steps (to see the problem):
1. open repro project, open SampleScene
2. In hierarchy, select "INSTANCE-FBX" > "SpitterMesh" gameobject
3. in inspector, check the value in "Inspector Enhancements" > "Exposed data" > "Skinned mesh renderer bone count"
4. note there are 135 bones
- in project tab, select "FBX" > "SpitterMesh (Mesh)" and check inspector > "Skin:" to confirm 135 bones on current FBX
- this prefab is directly instantiated from the FBX and is correctly updated when FBX is modified or import settings changes
5. in hierarchy, select "INSTANCE-Prefab-A-optimize-off" > "SpitterMesh" gameobject
6. in inspector, check the value in "Inspector Enhancements" > "Exposed data" > "Skinned mesh renderer bone count"
7. note there are 73 bones
- in project tab, select "FBX-ORIGINAL" > "SpitterMesh (Mesh)" and check inspector > "Skin:" to confirm 73 bones on the old FBX
- this prefab is instantiated from a prefab that was first created when the model contained 73 bones (before artist made changes to FBX)

EXPECTED: at step 7, the prefab using "FBX.fbx" model should have 135 bones on the skinnedmeshrenderer to work correctly with the new mesh
ACTUAL: at step 7, the skinnedmeshrenderer is shown to have the old bone list of 73 bones from the original FBX

Repro: 2021.2.16f1

Workaround steps (to fix):
- open the affected prefab ("Prefab-A-optimize-off")
- delete the "Skeleton" and "SpitterMesh" game objects
- still in prefab editing mode, drag and drop the FBX into the scene view or hierarchy (to instantiate the FBX inside the prefab)
- then close and save the prefab
RESULT: now, the prefab should contain a nested prefab which will be updated with any changes to the FBX

More info --

Steps (to create the repro):
- import an FBX with a skinned model (must have a rig and skinned model)
- drag and drop the FBX from project tab to the scene view or hierarchy - to instantiate the FBX as a gameobject
- drag and drop the gameobject from hierarchy to project tab to make a prefab
- choose "original prefab" from popup dialog
- also repro using "prefab variant" from popup dialog
- change the FBX rig somehow in authoring software (for example, delete 1 bone from the rig)
- export the FBX and be sure to overwrite the original (take a backup of original first, if needed)

Expected: prefab skinnedmeshrenderer component has correct number of bones according to the assigned model
Actual: skinnedmeshrenderer component in the prefab has old bones list (according to the original FBX used at time of creating prefab)