This peculiar problem occurs when a user attempts to compact his database, the message on the server is “error compacting (databasename): document has been deleted.” I ran fixup and updall -r on this mail database and they ran successfully. Afterward I retried compact and still received the error.
I also see this error - And in addition, the database does not replicate all changes - despite clearing the history, and ensuring the replication settings field “only replicate incoming documents saved or modified after…” is blank. Manually replicating produces no errors, yet the number of documents in the replicas differ by hundreds.The only solution I have is to delete the replica and recreate from the clustered server.