I am a bit confused by the problem.
Did you by any chance mean when people use the “Apply” instead of “Revert” button?
The revert button will revert the instance to be the same with that of the prefab, but the scene instance doesn’t lose scene referenes. unless of course the instance is reverted back to a prefab that doesn’t even have a node that for example was added to the instance, in which case the instance doesnt will lose the node as whole too.
Is the problem that people occasionaly forget to Apply the prefab? I can definetely look into making it more smart, but it would be great to know the issue better.
Furthermore I would like to let you know that in verison 1.6 prefabs are now editable, without the need to put them into the scene 🙂