To repair the indexing file of a folder:

• Right click on folder and select 'Properties'
• click on 'Repair folder' button
• click on 'OK'
• select another folder and then reselect the 'repaired' folder.

What version of Thunderbird are you using?

Well as this problem now has "progressed" over several years, the problem must somehow be in several different thunderbird versions (windows build). Right now it was 48.x or something and gotton updated to some latest 52.x, so the client software is kind of regularly updated via the built in auto-update mechanism. Although with Thunderbird this autoupdate trigger doesnt really seem to very quickly update/upgrade itself to always the latest, maybe the software upgrades are held back via some algorithm, coming in waves or similar ideas.

what account provider? yahoo, gmail?

it some larger local (country) provider, pretty mainstream there straightforward. I went into the affected folders and activated some more columns in the message list, and there is something called translated maybe like "order received" or so.

For example messages in one folder start in 2014. There is a mail that has order received column set to "one" (1) and then seven consecutive copies, with much higher orders four digit orders all of them, all identical copies of this order one message, then comes a new (different) mail with order received set to 2 (two) then seven copies of that one again, and those four digit orders again are higher than any (or each kind of matching) of the previous seven copies of the message #1 and so on.

Some other folders have only doubles or quadruples of messages. Also not the whole folder consits of duplicates or quadrupels or even quintuples where these doubled / multiplied messages appear.

These folders all carry lot of messages, be it in total size (2,7gig to up to 3,9gig folder total) shown in properties of the folder in the thunderbird interface) , or even have large size and many times, (some ten thousand of messages in one folder, but only a few thousand messages in some other affected folder).

also we have set pop3 retrieval from pop3 server to something like keep 7days worth of messages on server and delete all others/older ones.

Only this affected machine fetches this pop3 mailbox, so nothing else interferes. I guess once thunderbird retrieves a message via pop3 it gets flagged as retrieved and it gets expunged/deleted after 7days or the interval we set.

I dont think the user ever received the message(s) affected here in this bug many times over and always tiresome moved the message over and over and over (3times, 7times)? to the same folder inside thunderbird to keep order in their mail.

The user only reported these findings to me when they later observed that some folders carried multiple duplicates of the same mails after a while.

Any more to report? Maybe this needs a proper bugreport only I dont know how to reproduce or how to maybe submit some affected folder as the mail ist mostly private or sensitive contents :(

Any suggestions? Thanks.

what was the result of Toad-Halls suggestion to repair the folder?

The issue is caused mostly by anti virus scanning of emails, although less frequently a corrupt message on the server to be downloaded is the problem.

What happens is the download starts, the anti virus barfs or the corrupt message is encountered and the download does not complete so thunderbird does not get to update the local record of what mail is downloaded from the server (necessary because you do not delete on download.) The next mail get process downloads those same mails are again as they are not flagged as received.

This process only has a couple of default exists . one is the automatic cleanup of the corrupt mail by the provider, either by deleting the mail on their spam folder (The usual location) or some sort of server side maintenance that identified and removed the corrupt email. The other usual cause is the user deleting the mail that causes the issue either in web mail or on another device.

If the issue is the anti virus program, a computer reboot usually clears that. But there are reports for Nortons simply choking on certain malware mail and also causing this issue in that the download never completes normally to the mail arrives again.

All of this however only affects the inbox. It will not affect other folders unless the user moves the mail to a local folder or uses a filter to get it there. Are there message filters than may be placing duplicates from the inbox into other folders?