Update prefab instance with local values (Editor Script)

I am trying to update several prefabs via an editor script for local scene values. They are all good until I hit "Play". Do I need to somehow mark the prefab as dirty? The specific instance I am having issues with is updating the SortOrder on a SpriteRenderer. I really don't want to have to write a separate inspector class to handle this - I have one utility that does a range of modifications to the scene.

I also ran into the same issue with another prefab, and I ended up just breaking the prefab reference. My Utility script just grab references to all the components with the particular script, instantiate normal gameobjects from prefab, and delete original gameobjects.