Is there a new way to edit prefabs in Scriptable Objects? The old method seems broken in 2018.3

I had a prefab connected to Scriptable Object. In 2018.2, I was able to edit the Prefab using Context Menu functions that were called in the Scriptable Object. In 2018.3, the changes are not saved. Is this a bug or is the behaviour no longer allowed?

I am having similar problems about prefab references in scriptable objects. I was about to go crazy last night :frowning:
2018.3 look almost completely useless :frowning:

That is EXACTLY my issue! I have a context menu that loads the data into the prefab. Now the code won’t work unless I call PrefabUtility.SavePrefab. It works but it is very finicky and I gave to change a value in the Scriptable Object before the function will actually work.