There are files that list what files the game should be reading, but as long as your just editing them you wouldn't need to add these back in (since they have the same name), and if you renamed the originals then those won't be read. What did you actually change?
Starting units, starting cash, build slots on every planet to 8, max space stations allowed set to level 3, max gun satellites allowed to 5 everywhere. I did NOT change the pop cap.
I figured - like most games - when a mod is slightly off it won't start or will crash. Instead, what happened is as described above: as if nothing was changed. The two original files were renamed before placing the edited files.
I think that's it. Pretty standard modding behavior, just not standard game behavior (I assume). LOL