I got to thinking of a problem I had awhile back where messages I'd move would show back up in the original inbox. Rebuilding folders of course had no effect. One of the articles I saved had to do with rebuilding its cache.
Don't know if you've seen it or not, but I've kept the link handy just in case. Suddenly all emails are not visible | Thunderbird Support Forum | Mozilla Support
I ended up upgrading and haven't seen the problem since. Seems a lot of 'new' versions are a bit buggy. I've stayed at 78.10.1, which has been stable for me. Of course, a clean install may help clear things up. Backup your profile folder, then uninstall TB and start with a clean install.
Don't know if you've seen it or not, but I've kept the link handy just in case. Suddenly all emails are not visible | Thunderbird Support Forum | Mozilla Support
I ended up upgrading and haven't seen the problem since. Seems a lot of 'new' versions are a bit buggy. I've stayed at 78.10.1, which has been stable for me. Of course, a clean install may help clear things up. Backup your profile folder, then uninstall TB and start with a clean install.