What do you mean exactly? If you are referring to being stuck in separate maps, you should be able to save and then immediately load from it in order to reset the script to the correct one.
I'm gonna work with it a little and give it a forum thread, probably make the time-attack optional so that one can just mess around and not have to worry about dying, but I don't want to stray too much from Vanilla CS. Can't really fix bugs when the whole point is the intentionally break the game.