The last time I used branch deploys, I wasn’t getting any branches in the list, however, I still went ahead and entered my branch name and it works. Did you try that?
The list shows me the branchs from my old repo.
If I try to manually enter a branch from my new repo, I just have a message saying “No result found” but I can’t go further.
Not ideal but have you tried creating a new site with it linked to see if they work there? It could be that a bug needs to be filed when changing repos this occurs.
Thought I’d update you with a little bit of testing, if you make a change to the branches you’re trying to deploy, then deploy after you’ve added them to the deploy context they will appear. A bug I am going to report is that the old branch subdomains remain linked to the old repo.