Are the affected books ones you purchases from Kobo and loaded on with the desktop app? ADE?
I had about 50 DRM-FREE, regular epubs on my Kobo when I upgraded, and they all remained safely tucked away in the bookshelf. The two I had open before the update are the ones that stayed on my reading list.
Have you tried removing these books from the Kobo, and reloading them back on? Maybe the update does something funky with the database that causes these problems (a couple other people have mentioned similar problems). I'll try playing around with some of the Free Kobo books when I have a second and report back
(At least I can do this now without the sync messing up my other books!
