Outlook downloads messages from a Post Office Protocol 3 (POP3) server again after it empties the Deleted Items folder even if you have both the Leave a copy of messages on the server and the Remove from server when deleted from Deleted Items options enabled on the POP3 account.
This problem occurs because a background synchronization took place at the same time or just after the Deleted Items folder was emptied. This is an issue with the order in which Outlook carries out the deletion from the server and the downloading of messages.
There is not an available workaround for this problem other than not to begin a synchronization at about the same time that the Deleted Items folder is emptied. This issue does not result in data loss (other than messages that you instructed Outlook to delete). Simply delete the duplicate messages.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed at the beginning of this article.
When you enable the Leave a copy of messages on the server option and messages are downloaded, the unique ID numbers of each of those messages is added to a list of messages previously downloaded so that Outlook does not re-download the messages during future synchronizations. When the Deleted Items folder is emptied, Outlook removes the unique ID numbers of the previously downloaded messages from the list in preparation for deleting the messages from the server. If a synchronization (either manual or automatic) begins during this process, Outlook erroneously downloads all of the messages again because their unique ID numbers do not appear in the list of previously downloaded messages.
Article ID: 292249 - Last Review: Apr 20, 2001 - Revision: 1