Previously with Xcode 7.3.1 I was able to build directly over my app store app on my iPad and test the upgrade scenario, which worked perfectly fine. This week I upgraded to
Here is one solution if you want to upgrade over your existing App Store app without deleting it but your application-identifier entitlement does not match. Upload an archive of your new build to the App Store and then use TestFlight to download it to your device. This is not as quick as building to the device, but it will overwrite your old app with your new build while keeping your old data in place. For (relatively) quicker turn-around testing of your upgrade process once you have a new build available on TestFlight:
The TestFlight build overwrites the entitlement without deleting the old data, so Xcode happily will install your new build over the TestFlight build, but you are still testing your upgrade process as if you were building directly on top of the App Store version of your app.