When you use a classname in JavaScript, it does not look at the CSS to find that class. It looks directly in the HTML code.
All that is required is that the classname is in the HTML. It does not need to be in the CSS.
In fact, many people think it's actually a good idea to keep separate classes use with CSS and Javascript, as it allows your designers and coders to work independently without getting in each other's way by using each other's classes.
(note, the above paragraph is obviously more applicable for larger projects, so don't feel that you have to go to this extreme if you're working on your own; I mentioned it to make the point that the two can be entirely separate)