Try rebuilding/repairing your INBOX and/or other effected folders. Right-click on the folder in the left-hand pane, select 'Properties' and then "Repair Folder". This can happen when Thunderbird's cache gets out-of-sync from the server and it cannot figure out how to get back in sync on it's own. I used to get this quite a lot when using IMAP to access an Exchange mailbox (Exchange is a notoriously poor IMAP server)
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