I can confirm that KarlGoetz's workaround solved the issue in my case.
Renaming Inbox.msf caused a new Inbox.msf to be created, and all emails
were then viewable upon thunderbird restart. Generating the msf file
took ~30 seconds for a 2GB inbox on an average laptop.

For searchability, here were the symptoms that the workaround fixed:

 - opening a recent email (from yesterday) would actually open an older email 
with a very similar subject string (from 2007)
 - some emails were entirely blank - both body and header - and their source 
did not resemble anything like an email (it appeared to be a jumble of 
characters, maybe base64?)
 - some email text appeared cut off mid-sentence.
 - having any sort of media in/attached to an email seemed to cause these 
symptoms. The few plain-text emails I opened were unaffected (though I didn't 
test this thoroughly).

Oddly, the old msf file was 1.7 MB, and the new one only 1.4. Hope this
helps.

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https://bugs.launchpad.net/bugs/379629

Title:
  thunderbird corrupting email since 20090519

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