I was really hoping they'd address the whole "I'm Reading" list when a new book is added with the firmware upgrade. Everyone from Kobo that I talk to just tells me to delete it from my library and hang onto it online...it's like they don't realize that people actually want to keep them on their readers, not just online.
Anyways...the only way I work around this is when I do add a new book, in the desktop app I make sure all the books I've purchased and read are on the very last page of the book. That way when they re-appear on my list, all I do is open it up and have to click the next page button once to get rid of it. I've got about 14 books that I've purchased now, so it's getting annoying, but still better than removing it from the device altogether in my mind.