I learned not to touch the keyboard when TB was downloading new messages and running filters. Otherwise it would randomly corrupt the message file, and I'd lose it all. Yes, I filed a bug report with TB. No, they never found the problem.

I stopped using Thunderbird a long time ago because it had a “feature” that would erase all of your email if it detected that your profile was corrupt…

… but it has a habit of corrupting profile files on shutdown.

If all other explanations fail then even the least likeliest explanation is very likely true.

After all recommended approaches have been tried unsuccessfully, certainly the solution will be something that is not recommended.

I stopped using thunderbird for this reason