2018.3 Setting active state by code will not be saved in prefab

I have an editor script that gets the currently selected object and loops over all its children setting gameObject.SetActive(...) on anything that should be enabled or disabled by default.

This no longer works as the new prefab system will not detect it as a change, I have to manually change anything in the prefab and back again for it to trigger a save.

Is there any way to get this working with new prefabs?

 

Have you tried RecordPrefabInstancePropertyModifications already?
https://docs.unity3d.com/ScriptRefe...ecordPrefabInstancePropertyModifications.html

... or SetDirty?
https://docs.unity3d.com/ScriptReference/EditorUtility.SetDirty.html

 

Yeah, the old system i had used SetDirty and I added:

PrefabUtility.RecordPrefabInstancePropertyModifications(target.gameObject);

Neither does anything.