What I was thinking, that might make things easier as far the design is if you have the color scheme inherit from "something." Not really sure how yet using HTML5, but in one of my C# apps it just referenced a class that had a set of color codes in it, then, when you changed the "scheme" (red alert, primary, secondary, etc) all controls would follow and red alert would override all.
For example, if I was working in a "primary" section and triggered a red alert, the scheme would change and fire an event that updated all panels. Once red alert was cleared, I just needed to reference the primary scheme again and all controls would update back to the normal color patterns.
Does that make sense?
I think this would make sense in the simulator. For example, if the tactical officer triggered a red alert, the other panels on the bridge would switch to a red alert scheme. Once the tactical officer went back to green alert, all panels would go back to their associated system scheme.