We have reviewed the issue carefully and can confirm that this is not a bug.
In this case there should be a call to 'RecordPrefabInstancePropertyModifications'. Call this method after making modifications to an instance of a Prefab to record those changes in the instance. If this method is not called, changes made to the instance are lost.
The documentation is available here: https://docs.unity3d.com/ScriptReference/PrefabUtility.RecordPrefabInstancePropertyModifications.html