As long as you don't do anything drastic, your old mail folders are almost certainly still all there.
Have a look into
C: \Documents and Settings\<your name>\Application Data\Thunderbird\Profiles\<something gibberish>\Mail\<folder names>
If you find all that's "missing" is still in there, then create new folders under a new profile, then copy across the contents of the folders under \Mail\... and you should find all your stuff has returned.
Been there ... done that.