I agree that having to repeatedly trash and then replace your books on the Kobo desktop is a pain.
As I prefer to side load all my books onto the Touch including those purchased from Kobo I need to remove all the books from the I'm Reading section when I update or factory reset (sadly I've needed to do a lot of those!)
However on my iPhone and iPad I use the app so I need the books back in I'm Reading. It's very frustrating.
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