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If you want, you can completely reformat the user visible partition, (the part of the kobo that mounts as a filesystem on your pc), and re-start the kobo, the kobo will re-create what it needs to operate.). It's only a Fat32, so you can also run standard file system check utilities to verify it's integrity.
You can also initiate a factory restore on the kobo, (More Icon, - Settings - Device Information "Factory Reset your Reader.").. That will restore everything, including the operating system partition, from a backup image. But in this case, I have a really big caveat....
Based on your description of the problem, I suspect a failing storage device to be a high probability. Trying to do a factory restore under this circumstance is as likely to brick a device as fix a marginal one.
As for the database, it is unlikely to be responsible for the files going missing when you search from a pc. But if you suspect your database is causing issues, you can delete the database file at any time. (From the device, you can go into Settings - Accounts and "Sign out" of the Kobo Ereader, that will effectively do the same thing.). Please be aware that you will lose all your bookmarks, current reading positions, and probably other annotations.
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