Well it looks like the map editor just ate about 3 or 4 hours worth of work. I had all the systems in place, and was proceeding to put in the warp points when I saw that I had linked 2 systems incorrectly. So I deleted the warp point at both ends, and it went away. But when I tried to reconnect it to the proper system, the quadrant map showed both connections, and the system maps showed only the second connection. Now I am unable to even open the file (I got a read of address FFFFFFFF error), and I don't see anything I can do about it but start over.
Has this happened to anyone else, and is there anything I can do to keep it from happening again?