Currently, there are no options for Administrators to automate the change (or signal the change) of email domain for JIRA/Confluence cloud and Atlassian Accounts.

Ideally, there would be a streamlined process that will signal to Atlassian Account that there is a change if the email domain to be used by users. Signaling to end-users to choose to use the new email as the new email for their Atlassian Account, or to create a new one, with details on the instance that called for the change.