If you have updated your app over the MS dev-center, the package was accepted, but the app don't start on the devices after download the update from MS store anymore, you should read this thread:
http://forums.xamarin.com/discussion/52100/wp-8-1-deploy-error-package-could-not-be-registered-after-update-from-8-0#latest
If you have your WP 8.0 app already in the store and want to update it with a WP 8.1 package, you should read this thread:
http://forums.xamarin.com/discussion/50960/hints-for-update-wp-8-0-wp-8-1#latest
I have lost more than two full weeks of cause incredible problems and posted the threads to maybe help some other users...