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On the Kobo website in Canada, folks often delete the books they do not want in the "I'm reading" section (which puts them in the trash), sync, and then take them out of the trash.
From my perspective, a better bet is to load the books via ADE. When you then unmount the Kobo, the new books will be in "I'm reading". If you start reading them, at that point, the book will stay there. If you do not start the book (which creates a bookmark) the newly loaded book will slip back into the "Books" section, where they show as unread.
If you prefer not to use ADE, you will see the same behaviour if you sideload using Calibre.
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