If a user has dupicate messages they can be easily cleaned up with the following Thunderbird extension.
Install the plugin and connect to the mailbox which has duplicate messages using Thunderbird via IMAP.
Click all folders one time to retrieve the headers.
Right click the top level (above the inbox) and start the Remove Duplicates Plugin.
(+) has a linear algorithm, which means he removed duplicates out of my roughly 50.000 emails within one minute.
(+) can also compare mail bodies for advanced duplicates detection.