I finally got the QMC admin to test this with me and as you've said it worked perfectly. On Dev environment I published an App and kept a copy. On the published App users created sheets and some of those sheets were published to the community. On the copied App I updated and created sheets. Then asked the QMC admin to republish it and all new changes were there as you've mentioned.
I guess being new to Qlik Sense and thinking of an App as a file, makes it difficult for us to understand why this worked but we'll get there. Maybe the user created objects don't live in the app but in the repository as Simon hinted?! Another thing I guess we need to try is what would happen if some of the user created sheets that have been published to the community are approved to become Base Sheets? Will there be then a difference between the copy the developer has and the published app?
Thanks again for taking the time to respond,