When migrating a user mail file the message come over as already read, the unread marks are not maintained and in the migration log you see the error:
Warning: Unread Note Table Not Found
The user 's unread table is obtained by the canonical notes name in the Notes Full Name field of the Notes Migrator (NM) person document. The hierarchical canonical name must be the first entry in the Notes Full Name field.
If this is correct, then check the following:
If all looks correct, run the 'Fix Unread' agent from the 'Set Migration Profile' view in Notes Migrator. This will initialize the unread table in a staging replica.