http://kb.mozillazine.org/Disappearing_mail
"It's possible that the ".msf" files (index files) are corrupted. To rebuild the index of a folder, right-click it, select Properties, and choose "Rebuild Index" from the General Information tab. You can also close Thunderbird and manually delete them from your profile folder; they will be rebuilt when Thunderbird starts. "
Of course back up your profile before you start this. Good luck!