I downloaded a pre-release version of the iPhone SDK and tried to update one of my existing apps using a binary I built with it. Obviously you are not supposed to do this b
You need to download the release version of Xcode with the release iPhone SDK. You can't use the SDK downloaded from the iPad beta version for any release products.
Just go to http://developer.apple.com/iphone/index.action and click on iPhone SDK 3.1 and download it. Then build your app bundle with that and submit it to Apple.