For ShutUp10 at least (and probably the others): Yes. Microsoft resets settings when updates happen. The application explicitly warns you about this. And indee

For ShutUp10 at least (and probably the others): Yes. Microsoft resets settings when updates happen. The application explicitly warns you about this. And indeed, I ran the application before and after receiving the 'Creators Update' in my VM & some telemetry settings had been reactivated.