Interesting thing I learned about waypoints...

[Baron Munchausen]

Originally posted by geoschmo:
Yes Ed, I was not totally clear on that point. The confusion comes about because of the way the game gives newly constructed ships their move too orders. If you have a space yard with a "move too" assigned, any ships constructed at that base will be given orders to move to that spot, not to the way point. If you move the way point, any later ships built will be sent to the new location, but ships already built and on their way will continue to the original destination.

However, ships given orders by using the "move to waypoint" button will have their orders listed as "Move to waypoint x" instead of "move to N system(x,y)". Those ships will actually be redirected if you change the location of the waypoint.

Sorry I was unclear.

Geoschmo

I'd call that a bug and ask MM ot fix it. Ships should always be given the move to waypoint order when built by a spaceyard so you can make just such a change in mid-transit.