We have posted an update to the Packager for iPhone that makes it easier for you to build AIR apps for iOS and submit them to the App Store. Update 18.104.22.16840 addresses issues when submitting AIR applications for iOS to Apple’s App Store that resulted from changes to Apple’s application submissions tools. You can download the latest standalone Packager for iPhone from Adobe Labs. or get the Flash Professional CS5 Update for iOS from the Flash Support Center.
Update: Valerio from the Flash Professional team has posted a nice video walkthrough for updating PFI in Flash Professional CS5 and publishing an example app for iOS.