If you want community stories and sheets to remain you need to publish the new app by replacing the old one. When you delete and re-publish the app id changes and the community sheets are wiped. We ran into that issue too, we haven't found a way to restore them, but I would be interested to know if anyone has.
I recentlly tried the Repository Snapshot Manager to restore one of my server that have some documents with users sheets that wasn't been published and I didn't lost them.
So, if you follow this steps you will be able to backup/restore the user sheets:
- Go to the apps path in your server (C:\ProgramData\Qlik\Sense\Apps)
- Copy the file with the same id of your app
- Rename the file copied to whatever.qvf
- Go to QMC->Apps
- Import whatever.qvf
Now you will see all the sheets mixed as part of the document.
It will be good to know some feedback if worked for you!