Should users be logged out of their mailboxes during a migration?
Exchange Migrator 1.x
Exchange Migrator 2.x
Here is an excerpt from Chapter 2 of the Exchange Migrator User Guide:
The advanced technology Exchange Migrator uses does not require you to stop the Message Transfer service while migrating. Exchange Migrator provides better performance if your Exchange source and target servers are not running at full capacity when you migrate. Migrations also run with better performance if mailboxes are not open during the migration. If a mailbox is open during the migration, current activity in the mailbox may not be migrated successfully. For best results, run the migration during periods of low mailbox activity. Fastest results are observed when running Exchange Migrator on the target computer.
Although it is possible to migrate an open mailbox, this could have an affect on migration performance. If a mailbox is open during a migration and the current activity in the mailbox did not migrate successfully, you may run the post migration task 'Synchronize and Update Migrated Mailboxes' to bring over any missed data during the original migration process.
To learn more about 'Synchronize and Update Migrated Mailboxes', please see NETIQKB1365.