• Remove Duplicate Messages
  If you have duplicate messages (e.g. from merging folders or downloading messages several times) you can use this tool to find and remove them from the selected folder and its subfolder by rightclicking on a folder and choosing "Remove...
  in Software > Thunderbird with duplicatemessages thunderbird thunderbirdextensions
• Thunderbird: auto delete duplicate messages
  The add-on searches a given folder for duplicate messages and automatically deletes them by tagging all duplicates with a delete flag and one message with the keep flag.
  in Software > Thunderbird with duplicatemessages thunderbird thunderbirdextensions

duplicatemessages from all users