I know what you mean
Wish I could suggest something else (where are all the Thunderbird users?)
Some people don't have their email on the PC at all. It just looks as though it is because it's stored on the email server and is listed in Thunderbird when you open it.
Not sure that helps because if so it sounds like it all went from the server, but it might be good to know why to stop it happening again.
In the settings for that account if it calls it POP it's on the PC, but IMAP means it stays on the server.