How does Exchange Migrator handle migrating accounts with multiple mailboxes?
Exchange Migrator 1.x
Exchange Migrator 2.x
Exchange 2000 allows a user account to be associated with only one mailbox. If you are migrating objects to Exchange 2000, you must select one mailbox to associate with source Exchange 5.5 accounts. You can merge the primary mailbox into the existing target account and create new target accounts for any secondary mailboxes.
The only time NT accounts with multiple mailboxes come into play when using Exchange Migrator (EM) is when you've selected MergeBySamAccountName or MergeBySidHistory -- if you didn't select one of those options then the issue never comes up. If you did select one of those options, then EM respects the NTDSNoMatch in Custom Attribute 10, just like ADC. If that property is set, EM assumes the source mailbox should not be mapped to the existing target account, and instead it creates a new Active Directory account for the mailbox.
For more information on NTDSNoMatch utility see Microsoft's Technet article:
Q274173: XADM: Documentation for the NTDSNoMatch Utility