I've reset my ipad and lost all my in-app purchases

I recently had a problem with my iPad and the Genius at the Apple Store advised that I reboot my iPad "as new" (not from backup) and then get all my Apps again from the "Purchased" section of the App Store. I've done this, but now I seem to have lost all my in-app purchases. E.g. when you pay to get more levels on a game etc. Any ideas how I get these back?