A factory reset will indeed reformat the userstore partition, which is what gets exported over USBMS, and what appears to have been wonky on your device
And it's handled in a manner tricky enough, that, yes, you should trust the Kindle to do it, and *never* fsck it manually, as the only thing that's likely to do is b0rk it. (And don't even try *formatting* it yourself, as that will *definitely* not work).
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