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When mail is archived the documents are removed from the original database. This creates a deletion stub. The deletion stub tells Notes that the document is no longer needed on this database. When the original database replicates with the server copy the deletion stubs are supposed to be replicated to the server copy therefore removing the archived documents. It sounds like the replication of the deletions never took place. In other words the deletion stubs that were created locally were never replicated to the server . This usually happens due to the level of access of the entity replicating. It is possible that the entity replicating did not have delete rights hence the deletion stubs were never replicated.
Depending on how long it has been you need to be careful with how the issue is approached. Deletion stubs are kept only for up to 120 days (default 90 plus 1/3 of the value). If you replicate the original database with the bad replica server copy after the 120 days you risk re-pulling all of the previously archived/deleted documents.
It would be best to get your administrator to take a look and see if the best approach would be to possibly create a new replica.
Feedback response number RCAA9J7TJ6 created by ~Keiko Deskiburli on 04/15/2014