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I haven't had a factory fresh Kobo image to test in a long time. But I seem to remember, the quickest way to get a clean slate without entries that could not be removed, (books that were in my UI but not downloaded/removeable.), was to delete the database file on the kobo. A new file without any ghost entries would get created on reboot.
Since that will remove all bookmarks and reading progress, it might not be a desirable solution for someone who has been using the Kobo, but if setting up a new device in Sideloaded mode, and are faced with unwanted clutter, that's the quickest/easiest way to clear it.
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