Two possibilities come to mind: First, not all levels need to be rebuilt, just rebuild your main or first level with the desired max nexus. The max nexus size is allocated only once, at startup of the engine.
Second, did you try a forum search? The issue of assigning the nexus through the .exe command line has been discussed before on the forum. Here is one of several links: Changing Nexus In Exe
Hope this helps,
Cheers,
tindust