Respectfully, firstly, maybe it might help to take a few deep, slow breaths when you next encounter this problem :) This can help calm yourself down and trying to be as calm as possible when tackling computer problems is usually the most effective approach. Please be assured I have felt incredibly frustrated by computer problems so very often but unfortunately, it's almost never helped me solve issues.

Suspect the key phrase in your problem description is "always after some time".

Perhaps when emails are moved to other mailboxes, the mail server is not being updated to reflect these moves.

If that is the situation, the next time Thunderbird checks the mail server, Thunderbird sees mail it does not have in the original folder and downloads it to keep your original folder in sync.

This could create the impression of 'duplicates' that you are experiencing.

Most likely the best approach, to verify if this hypothesis is correct, may be to take screenshots of the details in Thunderbird's `Account Settings`.

If you can take at least one screenshot of the first view of `Account Settings`, this may help get the ball rolling towards a solution. One step at a time until the scenario becomes clear. That's unfortunately the only calm, slower than ideal, way to approach these problems.

Locking this topic, because this should be continued in the original post at https://support.mozilla.org/en-US/questions/1429712