A similar thing happened to my wife's Thunderbird emails recently. There are quite a few MozillaZine suggestions if you google 'Thunderbird emails missing'. The one that sorted it for us was:
- 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 Folder" 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.