This is mostly sounding reassuring. My wanted banking app is on a list of apps that people have successfully used on Graphene OS so it's probably ok, but yeh, definitely want to be able to go back. I guess I don't know what answer I'm looking for, but in the anecdote I started this post with, I was amazed that it was somehow possible for changes to somehow survive a re-flashing to stock. I really, really don't want that to happen.