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Leave the stuff in the .kobo directory alone; the entries in .kobo/kepub are those books downloaded (and managed) by either WiFi from the Kobo Store OR via USB from a Windows / Mac using Kobo Desktop.
The only time you should make do ANYTHING in the .kobo directory structure is if you're making a manual change to the Kobo eReader.conf file (.kobo/Kobo) or copying the files from an upgrade to the .kobo directory.
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