How to reproduce:
1. Download, extract and open attached project '1121500repro.zip'
2. Open 'SampleScene'
3. Observe the Material in the Skinned Mesh Renderer (in the Hierarchy: GameObject -> McNeal02 -> McNeal -> body_mesh)
4. Select GameObject, click 'Overrides' in the Inspector and then click 'Apply All'
5. Select 'body_mesh' again and observe the material

Expected results: The changes to the prefab were applied and the material was changed to the one selected
Actual results: The material reverted back to a material that was used before the change

Reproducible with: 2018.3.4f1, 2019.1.0b1, 2019.2.0a3

Note: If the project is opened with the material is in a changed state (before applying changes), follow these steps to reproduce a crash:
1. Select GameObject, click 'Overrides' in the Inspector and then click 'Apply All'
2. Press CTRL + Z to revert the action
-- Oberve the crash

First 3 stack trace lines of the crash:
0x00007FF622C6578D (Unity) PersistentManager::MakeObjectsPersistent
0x00007FF622C6531F (Unity) PersistentManager::MakeObjectPersistentAtFileID
0x00007FF6227AD2B7 (Unity) ObjectUndo::Restore