[Delete]

Check the Trash folder? Restore from your backup? It's easy to make a backup copy of your entire profile and you should do it regularly. I crafted a batch file that does it with one click. I'd be happy to share it.

If you use IMAP, the emails should still be on the server.

Not to say that it couldn't happen, but I've been using Thunderbird for decades and I've never had what you describe happen or heard of it happening to anybody anybody else.

[Delete]

Any computer data that you can't do without needs to be backed up. Data corruption and loss can happen with any program on any computer. It's not a question of IF, it's a question of WHEN. Thunderbird is not immune, and whatever email solution you eventually choose won't be, either. Like I said, it's pretty simple to make a backup copy of your entire profile, which will preserve all your mail, configuration, addons, everything. That's one reason I stick with Thunderbird. Wherever you end up, back it up.

There is a potential solution (not effective for already downloaded messages or AV that changes their flagging) - Settings > Enable "Allow antivirus clients to quarantine individual incoming messages"

Namely, that my antivirus program quarantined the entire inbox file upon detecting malware embedded in a single message. So I encourage people who encounter this issue to explore that as a potential cause. Thanks to those who responded for the help and patience.

Oh wow, yeah that makes sense. You could try restoring the inbox file from quarantine and then deleting just the infected message. Also maybe add the mail folder to your antivirus exceptions so it doesn’t nuke the whole thing next time.