If you perform changes to a Published app you should have the possibility to select your new sheets/stories and Publish them. They will then be moved from your content into what we call "Community Content" in the app.
Your users, provided they have the correct security rules, should then be able to see your additions to that section in the app.
An alternative way is that you duplicate your app in QMC, do changes to the core app and then you re-publish the app and choose to overwrite existing app. That will add your new additions to the published app in the Hub while still retaining any user created content.