Alf P. Steinbach wrote:

And I'm hesitant to just delete index file, hoping that it'll rebuild.

it'll be rebuild the next time you start Thunderbird:
(MozillaZine: http://kb.mozillazine.org/Disappearing_mail)
* 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 Index" 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.

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