I’ve been using the Remove Duplicate Messages extension a couple of weeks now. It’s working well apart from the fact that the Prefs dialog doesn’t seem to be working, or at least for the “Prefere to delete…” selection doesn’t get saved. I prefer the “unread” choice, so I dug inside the extension’s code and found out the line needed in Thunderbird’s prefs.js file:
user_pref("extensions.removeduplicates.prefereddelete", 1);
Just stick it in there, among other extensions’ settings. Make sure TB is not running when manually editing prefs.js, otherwise any changes will be overwritten when TB is shut down.