I was going to make a suggestion as well, maybe for a future issue but I know Mary Poplin has a tutorial that I think addresses this as well with a single track. Basically, it was a track for a person's eyes and when they blink of course, it goes to hell. She simply tracked to that point, then during the blink frames, she literally moved the entire mask somewhere else which maintained it's form, then once the eye was back open, she placed it back on the eye. I'd say this is the same as your beams, except then during those 2 frames or so, you could do those manually in AE with ease I'd say. I've used the technique.
Just a thought.
Eric