They make new prints of ride films on a regular basis. (But probably run them to death.) There is more than one copy around! The original negatives ought to be sitting in a vault at Disney or ILM.
It's a safe bet the ride makeover will put in HDTV screens and be able to switch "destinations", so I doubt the original footage will vanish completely either.
I gave someone on here a copy of my capture of the Gil Gerard special several years back. Wonder if that's what out there now?