Reproduction steps:
1. Open the user's attached project "SkyboxRepro.zip"
2. In the Project window open Assets/DATA/Broken/BrokenRefNull Scene
3. In the Hierarchy window expand the "BrokenRefNull Scene" and select "CLICK ME!" GameObject
4. Observe the "CustomScriptableObjectDebugger" script property "SEE BELOW" in the Inspector window
5. Close the project, go to the project's folder and open Assets/DATA/Broken/Buggy Scriptable Object.asset
6. Modify the file's script line 16 from "dummyVal: 4" to "dummyVal: 2"
7. Re-open the project and repeat steps 2-4

Expected result: "CustomScriptableObjectDebugger" script property "SEE BELOW" has no "[ERROR] customScriptableObject.customMonobehavior = NULL"
Actual result: "CustomScriptableObjectDebugger" script property "SEE BELOW" has a "[ERROR] customScriptableObject.customMonobehavior = NULL"

Reproducible with: 2019.4.16f1, 2020.1.17f1, 2020.2.1f1, 2021.1.0a9
Could not test with: 2018.4.30f1 (Multi-object editing not supported)

Note:
- In the script, the reference to the customMonobehavior in the prefab is now NULL even though in the Prefab it is clearly seen that the reference is valid