One approach is to delete the books from the Kobo Library via the Web. From the My Library view select the books you don't want and then delete them.
It removes them from the "active" library but leaves them in the tab labeled Trash. You can restore them from the trash at a later time.
I also think that on the device, if you go to Library view, when you long tap on a book you have hte option to Remove a book. If you then select to just remove it from the eReader it will still be on your account.
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