This issue is caused by the use of External Portable storage to get the data to another Domino Server. When the replica was created before being copied over, they might not have been created and completed correctly.
Sources at Lotus/IBM have stated in the past that this type of data transfer can cause issues with the Unread Marks table.
A good way to transfer Replica over to a new server is to use inbuilt Domino tools to achieve this.
It is also important to replicate between the two servers once the replicas have been created.
Refer to IBM Support Article - 27002920 - "The Architecture of Unread Marks in Lotus Notes" for more details.
Refer to IBM Support Article -21676207 - "Step-By-Step Troubleshooting Guide for Unread Marks" for more details.
