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I don't logout of the desktop software so the books don't disappear. What you see in the desktop software is what is on the Kobo server, that is what is referenced when you sign-in. It syncs with the server, rather than looking at the kepub directory on your computer, thus the download. No sign-in, no connection to the server.
This is also why you only see your Kobo books in the desktop software. Those are the only books stored on the Kobo servers.
I may have misunderstood your question, if so, well, I'd be willing to try again.
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