Just noticed a nasty patch of what looks like diseased bark..would you cut flush with the trunk and add some Bordeaux mix?
Since the stub you left rotted, it's likely that it went down : I would use Bordeaux mix (Again!!!) to paint the wound and seal it with wax, or any other sealant. I know that this last advice is controversial, but that's what I would do.
I think from now on when I prune, if the branch is more than a couple seasons old and if it is in that funky Y area, I will gnaw it down till it follows the natural curve of the good branch. Less distance for the new cambium to grow, and less mass to fuel rot. Sooner it is healed naturally less chance of rot and disease. I’ve seen my trees heal from some long shallow scars pretty fast.
I saved a few trees with colloidal silver. my peppermint tree was getting some bad trunk rotting. sprayed it with silver solution and it recovered. yrmv.
