So after working over the weekend on the expanded universe I have come to the conclusion it is best for the star locations not to change.
This is ONLY the locations, the intensity and the planets inside the system will change.
Why? The map of all 2,600 regions when its generated in binary form is about 100mb in size. The original test was 400mb in size.
So if a player were to play in three wars at the same time, they could have 1.2gb reserved. This also means the map would need to be downloaded for every war instance.
By keeping the locations the same, then the map can be condensed and multiple wars can use the same map. This decreases both the download for the players and the bandwidth for the servers.