This article will explain the recommended Mailbox migration order when migrating a Primary Mailbox and an Archive Mailbox for the same Exchange Oniline account. The reason for this requirement is to ensure that after a FullSync migration is completed a MailSync migration is performed for subsequent delta syncs. To understand the difference between a FullSync and a MailSync migration see this KB.
Mixing the migration scenario (Primary to Primary, Archive to Archive, custom folder and date filters) between mailbox migration tasks causes the sync state to only contain records of items processed in that pass. Anything skipped is not added to the sync table and previously migrated emails are no longer tracked.
When performing a mailbox migrations that includes archive migrations, it is important to know that the mailsync feature will not function as expected if an archive migration is run anytime after a mailbox is enabled for MailSync. It is recommended to run an archive migration at the beginning or the end of your migration schedule for users mailbox data.
What will happen if an archive is run after running multiple primary mailbox migrations for a user?
The answer is that this will remove MailSync mode from the primary mailbox, below is what happens while processing these tasks.
What will happen to MailSync if a new task is created to only to set forwarding, migrate only calendar, permissions etc.?
If Migrate Mail is unselected for any task after a mailbox is using MailSync, this will clear the sync state table and the mailbox will no longer be using MailSync. Any mail items deleted or moved between the last MailSync task run and the new task that had not selected Migrate Mail will be orphaned and will not be synced. When the new sync table is built from a successful Migrate Mail task the state will only include items processed from that date.
Will switching between sync modes cause duplication?
Yes, there is a possibility that duplication case occur if the email migration engine is switching between sync modes such s using MailSync and then later using FullSync to migrate the mailbox. The following is an example of how this can occur.
Scenario: Items moved within the source mailbox.
Any other factors that would clear MailSync?
The following if configured within the Mailbox Migration task would force the task to use SimpleSync or FullSync.
How to verify which Mail Sync option is selected for a mailbox migration?
What happens if the domain is moved in the middle of the migration, or a users email address is changed in the source or target tenant?
As of Wednesday March 4, 2026 you can update the UPN or SMTP address without impacting Mailsync after you run a Refresh Selected Accounts.
