According to the below Apple link, you can't use Xcode to test the update since it can produce a "frakenbuild" that is not the same as actually updating your app.
So you need to make an archive/.ipa and install that on your phone, over the old version to test the true update path.
https://developer.apple.com/library/ios/technotes/tn2285/_index.html
To make the development cycle faster, Xcode only pushes changed files into the apps it runs, and does not delete files from existing app-bundles. This makes builds significantly faster. But it means that using Xcode to install an app over an older old build can make a "frankenbuild" with legacy files it wouldn't otherwise have. This can cause problems during testing and mask bugs.