I did have the same problem as all of you are talking about.... To fix this, I did a factory reset, then I replaced the sqlite database, after that I logged on to the kobobooks desktop app and resynced the device....all purchased books from kobobooks were accessable at that point....but when I loaded my other books through calibre, they were locked and ADE wasn't alllowing access either. I uninstalled ADE, reinstalled it and reauthorized it with the kobo now everything works...but all old bookmarks were gone.
I have found over the years with working with computers, that sometimes the only way to cure a problem is start out with a fresh install and work from there....it can be a pain in the butt at times but doing everything from scratch in the proper order with no half measures or shortcuts usually brings success.
Hopefully this will help you as well before the garbage man gets the kobo
EDinNB