The current version of Thunderbird 22.214.171.124 has a major bug that causes some mail that is downloaded from the server to disappear in the email client. Thunderbird displays the number of new mails that is in a folder correctly, but when you click to open that folder, the new mail that should be there is not listed in it.
The first time I have read about this message was on the mozillazine forum where a user named soulek described the problem that he encountered after he upgraded the email client to Thunderbird 126.96.36.199.
One solution would be to downgrade Thunderbird 188.8.131.52 to a prior version which should fix this immediately. A better solution would be to download a nightly build of Thunderbird and use that. The bug was fixed and all coming nightly builds should include the bug fix as well. The most recent nightly build for example is fixed so that all emails will be shown correctly in the program.
Thunderbird 184.108.40.206 which will include the fix will most likely be released sometime in December which means the only way to fix this bug now is to either downgrade or install a nightly build.
You will have to do the following no matter if you downgrade or install a nightly build:
The missing mail should appear. Everything seems to have reverted back to normal for me using the above nightly build. Let me know if you encounter errors or if this method is not working for you.
Update: The MSF files that you are deleting are index files that do not contain the mails, just information about them. If Thunderbird cannot locate them, it automatically creates them anew on the system.
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