Before resetting replication, you must remove unreferenced files by selecting Object > Remove unreferenced files on the Vault Configuration window. Otherwise, the replication operation fails because it its trying to replicate files that are already present in the vault folder.

To remove all previously replicated content for a target site, select Object > Reset Replication on the Vault Configuration window. When you do this, all content for which replication rules are defined will be replicated during the next scheduled replication operation. The File Server site may still contain content that has been uploaded to its cache, and references to this content are not removed. Use this option with extreme caution before the site is scheduled to be unregistered.