There are some mailboxes in the source organization which do not appear in the Exchange Migration Project. After refreshing the source server and adding Recipients to Database, the mailboxes are still not visible.
The mailboxes also cannot be explicitly added to any synchronisation collections.
The mailboxes are hidden from the GAL (Global Address List)
Another possible reason could be that the mailbox resides on a bridgehead server, not on the source server (cluster).
Verify if the user is hidden from the GAL in the source. "Unhiding" the mailbox or moving the mailbox to the appropriate Exchange server in source should resolve the problem. You can unhide the mailbox in Active Directory by opening the Properties for the User and on the Exchange Advanced tab deselect the checkbox "Hide from Exchange list".
After this has been done, in Exchange Migration Project expand the source organization and navigate to the particular source server, right-click and select "Refresh". This will trigger a new enumeration of Active Directory and the mailbox should appear and be available for synchronization.