like it saif in title, i dont think this can be done, but could you activate and deactivate waypoints with swictes or zones??? this would allow alot more kinds of puzzle games to happen and stealth games...
EDIT: some examples of that are,
1 makeing boxes move into different zone that activate doors
2 have you walk in a zone that activates a guy to come around the corner
3 set it so when you walk into a room, somone dies.
4 be able to change lift paths ingame
IT WOULD BE AWSOME
but i dont think its possibkle
dont assume cause ull make an ass out of you and me!