If you select a prefab variant in the Project View, make a change in the Inspector and then attempt to revert it, a warning will be shown in the console and the change won't be reverted.

The PrefabInstance is persistent and can't be merged.
UnityEditor.GenericMenu:CatchMenu(Object, String[], Int32)

In order to revert the change, you have to open the prefab variant and revert the change in isolation mode.

1. Open Unity
2. Open the attached project
3. Find the Cube Variant Prefab in the Project View and select it
4. Disable the Box Collider component in the Inspector
5. Right Click the Box Collider component name and go to Modified Component > Revert

Expected Result:
The change to the component is reverted.

Actual Result:
The change is not reverted and a warning appears in the console.

Workaround: Ctrl+Z does the job

Tested on Windows.

Occurs on 2019.1.0f2, 2019.2.0a12