Steps to reproduce:

1. Open attached project
2. Open 'TestScene'
3. Select 'Hide Flag Test Object'
4. Turn on 'NotEditable' flag
5. Set undo mode to 'Register Complete Object'
6. Press 'Set HideFlags' button
7. Check 'Hide Flag Test Object' in the inspector and scene, that it is not editable
8. Open the edit menu to check the undo steps
9. Press the undo step, 'Set HideFlags w/ RegisterCompleteObject'
10. Check 'Hide Flag Test Object' in the scene, it should be editable
11. Check 'Hide Flag Test Object' in the inspector, the components still show as not editable
12. Deselect and reselect 'Hide Flag Test Object', components are still not editable
13. Save the TestScene
14. Reopen TestScene, 'Hide Flag Test Object' inspector now shows expected state

The same bug occurs with HideInHierarchy, HideInInspector flags

Reproduced with: 5.1.4f1, 5.2.4f1, 5.3.5p7, 5.4.0b24, 5.5.0a2