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.

Workaround

Source: https://community.atlassian.com/t5/Jira-Software-questions/Re-How-can-I-change-the-email-addresses-of-all-the-Users/qaq-p/1623688/comment-id/125415#M125415

In order to bulk change the email of the Atlassian accounts/users in your Atlassian site, you must first verify your domain to confirm you are the domain owner and the manager of all the accounts under that specific email domain. Once that's done, all the Atlassian accounts using that specific email domain are considered Managed accounts, so you can use the following APIs to bulk update those accounts:

• The Organizations API is available to list all the managed accounts in your organization. You can use this to enumerate the unique Atlassian account ID for each user.
• The User management API is available to edit individual users. You can use this API to edit attributes for a given Atlassian account ID using the PATCH /users/ {account_id}/manage/profile method.

The types of changes you can make with those APIs include:

• Enabling/disabling the Atlassian account
• Changing user email addresses or departments

For other bulk user management changes, we recommend using the User provisioning (SCIM) API to sync users and groups from an external system. The documentation for the SCIM API is also now available.

P.S: There are a few considerations that should be taken into account when updating a user's email address. You can check those in the documentation below:

Change Atlassian account email addresses