Hi!
You can clear licenses listed on the license management page by hitting the disconnect now link for those you wish to get rid of – would that help here? You could if you wished disconnect them all, then visit the license tab (within the events settings screen in your WordPress installation) and reconnect so that the correct URL is listed.
It sounds though like it shouldn’t be a problem in any case – if you’re only using the license for one site and that site is listed then, even if additional URLs are also present, everything including automated updates should continue to work as expected.
Let me know if that’s at all unclear 🙂