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I just downloaded the latest version of the Desktop Kobo app this morning. It syncronizes every time I launch Kobo (and that can take a while), but my previous books are still there. They're kept in the Appdata\Local\Kobo\Kobo Desktop Edition\kepub folder on Windows (and they have no file extension). The Kobo Desktop program simply doesn't deal with anything OTHER than the kepub format these days. The titles and other details (including encryption, filename, etc...) are kept in the sqlite db, but the encrypted epubs should be fully intact in that folder I mentioned. Rename one with a .zip or .epub extension and have a look. The text will be gobledygook, but the structure's all there... plus some extra crap.
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