Revamping MY Mobile Device Setup in the JSS

I am looking for input on how you all have your mobile device application scoping and user scoping set up ( preferably if you have VPP and DEP set up). If I were to drop my devices out of the scope for apps that are currently deployed I am assuming it will not be removed unless I pull the MDM profile off of the device (all of my apps have that box checked). I am most likely going to remove all scopes and rebuild to something that makes more sense to me and I am trying to be cautious as I don't want to inadvertently dump apps from client devices. I appreciate any response, thanks!!