I have done it all three ways, lol!
If I am doing a program with others, I try to stay on schedule with them, at least week to week. (Everyone has their own preferred rest days, and may shuffle workouts around to accommodate that, but by the end of the week, we've all done the same workouts.) In that case, I add on to make up with prudence. For example, Ab Burner could go on almost any day, since it's short and a different type than the others. I wouldn't add BiO to a day with Burn Intervals, but I would double up on a day with a ST workout scheduled. Recharge can go anywhere, as long as you have time.
If you don't have that many extra hours to spend working out in a given week, you could also spread your make-ups out over two or three weeks.
Leaving them behind is fine, too, though, because over the course of the entire program you do those three many, many times. Since the focus of CLX is strength and muscle building, missing them a few times won't really change your 12-week outcome.