Grabbed from here

Real fix

If the folder is severely corrupted, deleting the .msf file won't help much, and compacting the folder may just make things worse because Thunderbird can't reliably figure out where a message ends anymore. You'll typically run into this only with the Inbox folder. It's much more vulnerable to corruption because it frequently has both lots of messages and a high percentage of deleted (but not visible) messages. That's why it's recommended that you move messages you want to keep to other folders/child folders rather than keep storing them in the Inbox. You can fix the problem by replacing the corrupt folder with a new known good folder. These instructions assume the Inbox folder is corrupt but you can adapt them for any folder.

1. Exit Thunderbird and backup your profile folder using something like MozBackup.


2. Start Thunderbird.


3. Move all of the messages in the Inbox to other folders/child folders. You can select all of the messages using Control-A. If you have problems moving all of the messages, do it in multiple steps, where you select only a few messages each time.


4. Verify that all of the messages have been moved.


5. Exit Thunderbird and delete BOTH the "inbox." and "inbox.msf" files for that account. Leave "Inbox.sbd" alone. You can find where the Inbox folder is stored by looking at Tools -> Account Settings -> Server Settings -> Local Directory, or Tools -> Account Settings -> Local Folders -> Local Directory if you are using a Global Inbox. Its at the bottom of that pane, next to a Browse button.


6. Start Thunderbird. It will automatically create a new Inbox folder.
   While its possible to move the messages back to the (new) Inbox, its recommended you don't do that.