make a trigger:
Condition: true
On Activation: trig1 = true
then in the trigger that is activated first put this:
Condition: trig1 and (any other condition you have)
then in the trigger that is activated second put this:
On Activation: trig1 = false
idk about cancelling waypoints, you can use a move command to make the ai move somewhere though. so if you wanted to change the waypoint of an ai group put this in the trigger that is changing the waypoint:
On Activation: aigroupname move (getpos waypointname)
you will need to name the group and make a gamelogic/marker and name it waypointname (or whatever name u want, as long as its the same as the move command)
for more info look in the official command reference:
http://www.flashpoint1985.com/docs/comref_102002/comref.html