Hi, KillerFrogs. I'm not sure what's up with the "Invalid command line" issue (perhaps Chris knows more and can shed some light on that), but as for the game, if you have it registered on Steam, you can get the license key by right clicking on the game and selecting "View game CD key". If you have the key that way, then all is good and you can go ahead and reinstall without issue. Save files are in the save directory inside the game folder, so you can back those up by going to that folder and making a copy of the save directory elsewhere.
I'm not sure if this will work, but if you don't have your key, perhaps what you could try to do is make a copy of your settings.dat file in your AI War directory, reinstall the game to try to fix whatever is wrong with your current installation, and then put that settings.dat file back in to the folder. When you reinstall, I recommend installing the same version you had before and then updating from there.
Does that help?