Sometimes I have a strange behaviour with GitHub Desktop: when I delete a branch in GitHub Shell, the branch continues to shown into the drop-down menù of GitHub Desktop! ... same behaviour with the "Delete branch-name..." function of GitHub Desktop.
I solved with git show-ref
to list all refs
cf7c75b18e47a566f5bebccd3746f19fa426af4f refs/heads/master
cf7c75b18e47a566f5bebccd3746f19fa426af4f refs/remotes/origin/HEAD
540b3c8032f76ec13c84d6f40de885b996465dcb refs/remotes/origin/branch1
cf7c75b18e47a566f5bebccd3746f19fa426af4f refs/remotes/origin/branch2
when there are the ref to remote, GitHub Desktop can't delete at all the branch.
You can't remove a ref with git update-ref -d refs/remotes/origin/branch*
and then you have
cf7c75b18e47a566f5bebccd3746f19fa426af4f refs/heads/master
cf7c75b18e47a566f5bebccd3746f19fa426af4f refs/remotes/origin/HEAD
Now you can remove the branc with git branch -d branch*