As both the owner of dogs that occasionally stay other places, and the person who takes in other dogs: meh. Offer to repaint her door. If they have kids and dogs, that’s minor stuff. If I were the sister, I wouldn’t think that was world-shattering, or something to end relationships over. Your dog has issues from his puppyhood. So does my pound puppy (same thing with enclosed spaces, dark figures). She knows his history.
If your dog is fine with other people, you should have other people watch him while you’re away.
We own a house that has two units and we stayed in one for a few moths while renovating our house (where we live). The tenant above was mortified that her dog has clawed her front door really seriously. We’ll have to replace it when she moves out. But the dog stopped and never did it again. Until…
Our tenant has three dog sitters. They come (well, only one at a time) and live at her home while she travels on business. The dog ONLY claws at the door when the one guy is dog sitting. We were living in the lower unit a few times when he has sat, and he’s really nice to her, spoils her rotten and she is always over-the-moon happy to see him. And every time he leaves the house, she tears at the door. We have no idea why. She does it for no other human and in no other circumstance.
You need to work at it until it takes. It’s not impossible to get him used to it; it just might take longer than you think. Just remember who’s in charge. When I worked in a pet store, people would tell me things like, “Oh he won’t eat dry food. He only eats canned.” I’m like, “Uh, so he knows how to use a can opener?” The issue is almost always one of when the owner gives in, rather than what a dog will or “will not” do.