Thought about this one a bit, had to do something at work other than fall asleep.
Two waypoints with the x values the negative of the other, i.e waypoint 1 at -10000, 0, 20000 waypoint 2 at 10000, 0, 20000
ship starts heading towards waypoint 1, when < distance reached, using the set-object-position and invert the ships x pos, clear goals and say to head towards wauypoint 2. When < distance reached, switch the x position and goal back to 1.
Repeat.
If the path to the second waypoint is not in camera view the ship disappears when it's heading towards it.
With a couple of variables, and everytime can be implemented in using just two events.
Example in the attachment
[attachment deleted by ninja]