I had to submit an update to an existing app (WARP gce was approved!). When I built to test the app on my device Xcode 4.0.2 gave me a signing error, something about the code_wrapper. So I tried just re-installing Xcode 4.0.2 and the error was fixed (most likely because Xcode 4.0.2 wrote-over whatever tools the beta installed). I did not try and run the beta, as I was still focused on getting the update submitted. So, archived and then submitted to the store and Xcode reported a confirmation but a few minutes later the App Store rejected the binary. Here is the verbiage:
Invalid Signature - Make sure you have signed your application with a distribution certificate, not an ad hoc certificate or a development certificate. Verify that the code signing settings in Xcode are correct at the target level (which override any values at the project level). Additionally, make sure the bundle you are uploading was built using a Release target in Xcode, not a Simulator target. If you are certain your code signing settings are correct, choose "Clean All" in Xcode, delete the "build" directory in the Finder, and rebuild your release target.
In addition if you thought you'd like to try and check out iCloud and updated your profiles, you cannot submit to the store. Remove the enable for iCloud setting and update your profiles to fix. Here is the error I got back for that error:
So in summary: you can run both copies of Xcode on your Mac but if you need to submit to the store you may need to remove the beta and reinstall 4.0.2.Invalid Code Signing Entitlements - Your application bundle's signature contains ubiquity code signing entitlements that are not supported.Specifically, value "( xxxxxxxxxx.* )" for key "com.apple.developer.ubiquity-container-identifiers" in is not supported.
If I find anything more about this I will update this post. There are a few discussions on the Dev forums I'm watching and participating in.