Most POP3 mail accounts can also be accessed from the web as well. (Check your e-mail provider's website). If so, you'll still be able to access your mail there.
Also, try opening your e-mail trash file with a text editor (such as Notepad). I've no idea whether it will work with Thunderbird but the equivalent file in Outlook Express often retains old e-mail well after the PC owner thinks they've been deleted.
Lastly, if you've got Outlook or Outlook Express (or any other e-mail client except Thunderbird) on your PC, try configuring it to download your mail. (It sounds as if Thunderbird has registered the fact that you've already downloaded these e-mails. Other clients will be unaware of this and should be able to access them).
Chris