Hmm....
Personally I'd throw the script out the window and use a branching waypoint tree using a script trigger.
To do this, have your first path of waypoints (the first option), with the last one as a HOLD waypoint.
Then make a switch type trigger, and sync it to the HOLD waypoint. Now make your second path of waypoints after the HOLD waypoint.
Now if you set the trigger to go off, you'll get the second set of waypoints. Otherwise you'll get the first.