To make ThunderBird automatically handle possible duplicate emails, you can edit the value of "mail.server.default.dup_action" in its prefs.js (or use its Config Editor) :
* 0 - (default value) retrieves duplicate mails like normal mails.
* 1 - duplicate mails will be deleted automatically once retrieved
* 2 - duplicated mails will be moved right into the trash
* 3 - finally marks duplicate mails as read
To remove those duplicate ones which has already been retrieved, you should install the "Remove Duplicate Messages" add-on.
4 months ago