Can I create a GameObject( or preferably a Prefab) that won't update a nested prefab?

I have a hint system I've built that adds a collection of scripts, components and GameObjects (which I will refer to as Hint) to a set of objects in the Scene. Adding everything works, but most of the objects the hints are being added to are prefabs. I was wondering if there's a way to tag all the hints so that when I update the prefab the hints there's something stopping the prefab from seeing these new additions. I know I can manually choose what I update the prefab with but was hoping for an automatic solution.