I don't know quite what you were asking. Yes you will lose root which means you will lose access to all of your root apps but once you reroot they will be accessible again.
I'm excited for its release. I'm hoping that it does replace the need for all these skins. The only good one is HTC Sense. Blur is eh. Touchwiz is whack.
So the removal of them will definetly be of benefit and will def refine the android os.