I've seen the suggestion to remove duplicate emails one by one. However, if you delete a duplicate, the original email will be deleted from the mail server. You would have to set the email to NOT delete the server email when the email is deleted.
My problem is ATT.net changed their setup requirements by changing the Pop and SMPT entries to simply Inbound.att.net and outbound.att.net. When this occurs, it will re-download all the emails that you have downloaded before. On one of our important computers, the emails went from like 6,000 to 28,000 emails. It will take almost forever to delete these duplicate/triplicates!
I am having the exact same issue with a client's @bellsouth.net address. Had to change those settings and it duplicated all 22,000 emails to increase total box to 40k... The client wants to keep Windows Mail (on Vista) as opposed to changing the email client (my suggestion: Thunderbird with duplicate removal addon).
I CANNOT find a completely FREE software to remove the duplicates so I may end up purchasing "Dupe Remover for Windows Mail & Outlook Express. Here is the link if anyone's interested, http://www.topalt.com/duplicate-remover-outlook-express-windows-mail.