Are the messages gone, or are there filters in place that make them hidden? Check that View/Threads is All, and there are no filters applied by the Quick Filter Bar.

Thanks for responding to my request for help.

No filters are being applied to those folders. I checked. The messages are just gone. I have no idea why they disappeared. I didn't change any setting or anything else.

If you (or anyone) has any idea how I can get those messages back, I would be grateful.

Is the account POP or IMAP? Is there an antivirus app that scans the profile folder, and possibly quarantined the folder due to a single message declared 'infected'? TB stores an entire folder in a single file, so if one message is flagged, the whole folder is affected.

Help/Troubleshooting, Profile Folder, Open in Finder, close TB, open the Mail or ImapMail folder where the folder were stored and see if the mbox file - the large file with no extension, named after the folder - is present.

The account is IMAP.

I followed the procedure you described.

For one of the empty folders, there is no mbox file. For the other empty folder, the mbox file contains only 13kb of something (obviously not all the missing e-mails).

I have Avast installed on my computer. I don't see any way to determine if it's quarantining anything.

If it's IMAP, does the folder still show in webmail? A folder in TB would have no mbox file, just an msf file, if the folder was set to not download message bodies (Synchronization & Storage settings), but you would still see the headers.

Here is an old reference on how to restore quarantined files in Avast:

https://forum.avast.com/index.php?topic=185374.0

You should exclude the TB profile folder from AV scanning, with Avast or any other AV app.

https://wiki.mozilla.org/Thunderbird:Testing:Antivirus_Related_Performance_Issues#AVAST

I tried accessing webmail using my laptop, and the e-mails that have gone missing on my desktop are still there. The folders appear and so do all the e-mail messages in them. So at least I can access them this way, if need be.

I opened the virus chest in Avast, and I don't see a quarantined file that seems to have anything to do with TB or e-mail. There is only one file with a 2021 date on it, but the label on this file says "Other:PUP-gen[PUP] Daisy Disk." Could that somehow be related to TB? (I do have Daisy Disk installed.)

I'm not familiar with Avast's quarantine process or Daisy Disk, but I suggest you disable or remove Avast, or at least disable all actions on the profile folder, then move the missing messages to new folders in webmail, then subscribe to those folders in TB.

I went into webmail and created new folders with new names. I moved the e-mail messages that vanished from my TB folders into those new folders. Then I went back into TB. The newly created folders appear, but there is nothing in them (even though I can see in webmail that they're full of messages). I subscribed to those new folders, but this doesn't make any difference. No e-mails appear. They're still gone. Of course, I tried closing and reopening TB. I tried restarting my computer. Nothing helped.

I got rid of Avast. Made no difference.

As an experiment, I sent myself a test message. When it came in, I dragged it to one of the folders from which my old e-mails disappeared. The test message disappeared, too. It seems that e-mail messages disappear as soon as they're put into one of the "black hole" folders.