I have a pull request that is requesting a merge into master from my branch, but the owner wants me to change the request to merge into a different branch from my branch.
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If your branch is (still) available remotely, you do not have to create a new branch locally.
Select your branch (which bears the changes you are submitting) either directly from the drop-down menu or under "# branches" (https://github.com/account/project/branches).
Click "New pull request". This lets you choose a new base (target) branch.
Here is a screenshot of Github's new interface:
I can submit a PR of branch UX
against any fork/branch---it doesn't matter whether I previously submitted a PR for branch UX
.