I think I had the same problem. I had to restore the sqlite DB (using the sticky above) after I screwed up trying to hand-edit. It took multiple iterations of syncing before all 40 of my books have been restored. Looking at the progress screen, they seemed to be copied in reverse order of acquisition, 2, 3, 5, whatever, at a time.
Now, to see if I can use Calibre to take most of them off the I'm Reading list. I tend to prefer the Kobo format to most of the ePubs, so am trying to stick with the desktop application.