Moved TB profile to updated OS, the same new messages keep downloading repeatedly. Why?

LinuxMint17, updated from LinuxMint16 (hard drive wiped and renistalled). Home folder (including TB profile) restored successfully. Previous emails display properly, and new (POP) messages have been retrieved, but these same messages at downoaded repeatedly, with every "Get messages" check. Same problem at two different mail servers.
Already over 200 duplicate messages in less than a hour! Shutting down Thunderbird until I get a fix.

I had just found that article when you posted the link. When I tried to delete the popstate.dat files and couldn't do so, I discovered the real problem:
Somehow, when the backup program saved the ''Mail'' subfolder to the ''~.thunderbird/e1aq0j8l.default'' folder, it set all of the files in that folder as Root ownership, including the popstate.dat ones, which prevented Thunderbird from updating the POPstate of each server.
I changed the ownerships back to my regular user and group and everything is working fine.

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