if the user goes to uninstall the app it'll remove everything
Isn't that the meaning of the uninstaller?

because any new files from these update installed will all be registered under the app
What do you mean with registered?

Then the only thing that I can think of is:
1) if remote > localApp then execute downloader, terminate localApp
2) once file is downloaded (100&#37 run the update MSI (silent).

I don't know how to run it silent with the Package and Deployment. but once it is done it needs to start the app... Hmmm... Needs more thought.