Will our Apps still be connected to the Media Cloud if we buy them out for full ownership?

If you buy out the Apps to receive full App ownership, you will have the capability and permission to modify the code or replace each App. If the app code is modified or replaced, you might not be able to control your Apps via the Media Cloud in the same way as before. 

If you keep the App code as is, you will still be able to control all your Apps via the Media Cloud.