I assume remove duplicates is an addon... this site supports Thunderbird not addons. I suggest you address your issues to the addon author. However what a computer is programed to see as a duplicate and what you think is a duplicate can be two entirely different things. FOr instance each email has a supposedly unique header field called Message-ID: I do not know is your addon uses it or some other metric. but even the message id can be messed with by software other than Thunderbird so it is changed so even those messages would not be duplicates in an addon I wrote to do the job. Given there are at least two current remove duplicates addons I really can not guess anything else. https://addons.thunderbird.net/en-US/thunderbird/addon/removedupes/ and https://addons.thunderbird.net/en-US/thunderbird/addon/remove-duplicates/ One certainly appears to have user defined "duplicates".