My wife deleted the iBooks application. I was sure I lost all books and Magazine. I Re Installed the App, and opened it. 1st sign of hope was that I noticed all my Collections were still there ( a list of about 15) I noticed the iPAD is working hard on some background job. Left it that way, and after 26 minutes all books and magazines, started to show up in the relevant collection. So. The books are not part of the application. Also not the collections and the pointers to the books. Just wanted to let you know.