Same here. It's only the inbox which is affected so the trash in the trash box goes back years whilst the useful stuff has disappeared!

It sounds like your mail files got corrupted.
Try to rebuild the index file of the troubled folder. Right-click the folder - Properties - Repair Folder

Note: depending on the state of corruption messages in the affected folder may not be recoverable anymore. In that case you'd need to restore them from a recent backup done prior to the corruption.

Corruption is often caused by anti-virus software messing with Thunderbird mail files. It is therefore recommended to create an exception for the Thunderbird profile folder, so that the real-time scanner won't attempt to scan the profile with your mail.

Also make sure to backup the Thunderbird profile on a regular basis