It sounds like your male is afraid of her now. It does happen, even with very tough dogs. It sometimes helps if you muzzle the female and have someone hold her so that she can not move around and smell him. (Even if she is not aggressive now, he does not know that. It may help him to see you in control of her.)
But this is not always the case. I saw this happen when a male Sibe jumped over a fence and attacked the breeding male before he had mounted. He was so nervous after that incident that he would not breed.
The best solution is to use another male for breeding. Since he was intimidated by this female, he may never have a problem again.