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I just downloaded this and used it to fix a large Sent folder and another Sent subfolder which had been corrupted with duplicates and was slowing Thunderbird. As long as you don't overwhelm the Remove Dup Messages add-on with a huge number of sets (duplicates) it is great and reliable.
I found that it still worked on 40,000 messages with 14,000 duplicate sets.
I've tested the extension with over 90,000 messages, but not as many dupe sets as you had. Good to know :-)
Also - readers should be reminded that if you include message bodies as a comparison criteria the extension would be much slower (although it should still get through them eventually).