There's no reason to remove him. He typically wont harm her or the eggs. They are extremely communal and will be happier together. Whoever thinks beardies need to be kept alone is crazy. They live in large groups in the wild. We often see that when their raised alone they stop eating between 1 and 2 years of age. They only start eating again when they have another dragon with them. It is possible to raise them alone and have them live happily but they are programmed for communal living.
Also if the mating did take, you'll get 3 clutches regardless of whether or not they're tanked together. They store the genetic material. So there is no need to cycle.
When she gets close, you shold be able to feel the eggs. If you gently feel her stomach it should feel almost like there are marbles in her. She will stop eating about 3 days before she lays and start digging a lot. Give her the lay box as soon as she goes off food. She may want to lay sooner.
Sometimes the first clutch is always viable so don't get discouraged
Hope that helps!