When you program an new remote, all old remotes will be overwritten. Only the remotes activated at the time of reprogramming will continue to work.
I know this because the little loop that the jump ring goes through broke on both of my brand new (in 2002) Expedition remotes. I bought pretty red new fobs from Amazon, thinking I would program the red ones to my wife's Focus and I'd use her old "ugly" black ones. Well, when I started reprogramming, she suggested that I see if all the remotes could be made to work with both vehicles, and they will. I suppose one remote could be paired with an infinite number of vehicles, because the remote doesn't learn anything. The vehicle computer learns the remote. The Expedition and the '09 Focus both will learn up to 4 remotes.