Yes, everyone using Thunderbird has this problem (with any antivirusprogram) since this is really a Thunderbird issue because of the way TB stores its mails.
There is however a very simple solution: Let's suppose your in Thunderbird. You see your inbox, outbox, sent, trash. Now what you should do is create a new subfolder and name it for example "mail", "private", "work" or anything you want.
Once you've received a message and read it, you move the message to one of the subfolders you've created.
This way, when your inbox gets deleted due to an incoming virus you still have all your previously received messages.

Simple isn't it ?