Films, App's and Music gone after Updating iTunes on 21/02/2013

Yesterday I updated iTunes and the latest OS for my iPad and iPhones. All my books, films and apps are not showing up in iTunes and the majority of music has gone. I have run back up and the problem remains with nothing apart from a few albums that are left. My iPad still has the apps, films and one play list. I presume if I sync now with iTunes I will lose all that? How do I recover the missing files?