I have been working with Domino for quite some time as a developer. We encountered this problem recently, using Domino 5.0.10. We had a critical application which had replicas on quite a few servers. One day some agent ran and all the documents in one of the replicas got deleted. So we stopped replication and had the database restored from backup. Things worked fine for a few days. Then we had the problem of duplicate documents getting created. We were unable to figure out why this was happening, as the document properties for the original document and the duplicate documents were identical. Why do duplicate documents (not conflicts) get created when scheduled replication takes place? We usually notice this when a new replica is created or when a database is restored from backup.
Most likely, when you did the restore from backup, you created "new" documents, which were not true replicas of the existing documents. I suspect that close examination of the documents' IDs would show this. You probably need to fix things manually to remove the duplicate copies.
It sounds like you already know this, but for the benefit of other readers, replica databases are NOT a backup mechanism, for this very reason. If you make a mistake and delete some documents, the other replicas are very likely to "get" that change and also delete the same documents.
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