[Taz-in-Space]

Gryphin, I have experianced what you describe with the Map Maker. After some testing I determined that the problem comes from having Warp Points(WP) in a system having nowhere to point to. By that, I mean the systems that you deleted had WP pointing to them from other systems. I also suspect that, unless you deleted the contents of those 2 systems, (planets & stars, etc.) that you have somewhere on your map systems with the contents of the deleted systems included with their own. You can tell this because the planets and stars will have their old system's names still.
What this means is NEVER delete entire systems without deleting the contents of the systems first!
As to how to fix said map - I think it will take a shorter time to make a new one! Sorry, but it's true.