ex-Stash developer here.
Yes and no. Creating the branch though the UI is just a convenience. The important thing is that the name contains the JIRA key. If only one developer is working on the branch, it's fairly easy to just rename (delete + add) a branch with the appropriate name.
git checkout old-branch
git push -u origin old-branch:JIRAKEY-1234-something
git push origin :old-branch
Does that help?
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