When applying ProBuilder edits to a prefab, the Mesh and Mesh Collider data does not get applied.

To Reproduce:
1) Download and Open Repro.zip
2) Open SampleScene.unity
3) Select the "Test Prefab" prefab instance in the Scene Hierarchy
4) Click on the "Overrides" drop down in the inspector & click the "Apply All" button
5) Click on the "Overrides" drop down button again.

Observe not all changes were applied successfully. Expected result would be for the Mesh and Mesh Collider to be applied to the prefab.