Hi LorenzoJ,
Erik is correct. When you remove a player ship, all of its waypoints are also removed. Fortunately, when the waypoints are removed, the objects, such as areas, remain. That saves some work.
You need to make a note of all the parameters and conditions of every waypoint so that you can re-make them for the new ship.
Now for the bad news: The editor has a tendency to mess up its internal lists whenever objects are deleted. Make sure you keep a backup copy before you make any changes.
You can download the Mission Editor tutorial in PDF form here:
http://80.95.161.114/shipsim/forum/index.php/topic,2886.0.html (http://80.95.161.114/shipsim/forum/index.php/topic,2886.0.html)
You might want to download the Missions Manual also.
Regards,
Marty