The breathing stays the same. You may become less aware of your breathing at different times, as you exercise and enter deeper meditive states. When your awareness of your breathing comes back, you may tune into it again, and then drift again.
I would complete each exercise/meditation. At the end of the meditation, the harvesting qi aspect is simpler than after the active exercises. I view that part in the active exercises as very significant in terms of completing a total physical self healing session, where as after the meditations, I experience it as a shortened version way to "wake up" and come back into the physical body, becoming clear and alert, physically present.
