Our organization initially had JIRA but not Confluence. We recently added Confluence but used a different account because we were changing who paid. After connecting the accounts, we migrated JIRA to the new URL. The accounts were successfully connected. Links back and forth work exactly as expected with the exception of the Confluence workbox notification links going back to JIRA. Those links (and only those) are still pointing to the old JIRA URL.
We removed the links and re-linked JIRA to Confluence and Confluence to JIRA trying to force the workbox JIRA links to update, but nothing changes.