Are you using POP or IMAP? Messages are deleted from server with POP accounts if so specified in settings, but I am unaware of any setting that deletes after being read.

I have a POP3 connection. I see no setting in Thunderbird that allows me to delete emails after being read.

There isn't, although you can have messages deleted from server after being downloaded.

This deletion was working before I replaced the software for Thunderbird with the latest version. Maybe, there is a bug in it somewhere?

Now I am seeing that Thunderbird does not see messages sitting available on my server. I have configured Thunderbird to have the proper addresses of this server, so why can't it read anything?

OK, I found it. A setting in Thunderbird that says 'leave messages on the server'. Unchecking that did indeed remove it from the server as it was read into my Thunderbird folder. I think I am ok with this, for now.

Now, if someone can pull a rabbit out of the hat and help me restore my lost emails, that would be wonderful.

You have posted a new issue, so you should provide more info on how you lost them.