Your apk / ipa is configured to connect through the application url. If this is a custom url (not being mendixcloud.com / mxapps.io) then it will just connect to the correct application as long as you keep that updated.
However, if you're connecting to a default mx cloud url, then you'll obviously need a new apk / ipa. What you could do in advance is to already create a custom url, that's used by the mobile app. You ask the users to upgrade and when you move to the On Premise instance, you'd just have to change DNS.
The app uses a link to start up the application which is hardcoded in your distribution. You will have to redistribute to change/update that link.
Possible fix for the future:
You might want to try and manually edit that link in the phonegap build package and let it refer to a forwarding service that you can control. With this setup, you can change the url at any time without having to redistribute.