To reproduce.

1. Create prefab.
2. Delete its asset.
3. Unpack prefab instance of this prefab.
4. Press undo.

Expected result: After undo, prefab is shown as red missing prefab instance.
Actual result: Nothing changes after undo.

Seems that the PrefabInstance object is not properly reconstructed when looking at the debug mode in the Inspector

Reproduced on: 2019.1.0a11, 2018.3.0b12, 2018.3.0a6

Scenario 2

1. Create any gameobject and make a prefab of it.
2. Delete the prefab from the project window.
3. Delete the prefab instance from hierarchy. (It appears red because of the deleted asset)
4. Undo. (Gameobject appears in the hierarchy)
5. Make a prefab of the restored gameobject by dragging it to project folder.

Expected Result: Errors appear in the console.

Stack Trace:
1. AssetImporter is referencing an asset from the previous import. This should not happen.UnityEditorInternal.InternalEditorUtility:ProjectWindowDrag(HierarchyProperty, Boolean)UnityEngine.GUIUtility:ProcessEvent(Int32, IntPtr)

2. Assertion failed on expression: '!GetPersistentManager().IsStreamLoaded(metaDataPath)'UnityEditorInternal.InternalEditorUtility:ProjectWindowDrag(HierarchyProperty, Boolean)UnityEngine.GUIUtility:ProcessEvent(Int32, IntPtr)

3. Asset import did not unload metadata path. This will leak memory. File a bug with repro steps please. (Assets/Cube.prefab)UnityEditorInternal.InternalEditorUtility:ProjectWindowDrag(HierarchyProperty, Boolean)UnityEngine.GUIUtility:ProcessEvent(Int32, IntPtr)