Deleting systems in the map editor causes screwy things to happen like warp lines reconnecting to new systems, and planets being moved to different systems. Has nothing to do with the mod. This is an old bug. Malfador never really got the kinks worked out of the editor. Nothing I know can be done to prevent it.
The unimportant issue is just that, unimportant. Not a lot can be gleaned from viewing the map on that screen. You really only get an idea of the shape of the quadrant. Not exactly cheat worthy information. Plus, if the game ower wants to cheat there are a lot easier and more informative ways he can do it.
Geoschmo