No, he does not know she is his mother. He may be trying to prove that he is the dominant chicken of the flock. He may feel she is somehow defective and needs to go. Frankly, more likely, he is simply a "mean roo."
I have never heard of "rotating" roosters, though sometimes one can be put with a different flock and their behavior will improve. When a chicken is added to a group, it usually enters at the bottom of the pecking order.
You need to separate the roo to stop the behavior, as the hen may well be seriously injured or killed. You could try reintroducing him after several days.
Many roos have an aggressive streak that cannot be changed. It is generally felt here that these should not be bred, as it is often an inherited trait. If you try separating and reintroducing, and it does not work, he needs to be culled from the flock. I'm using "culled" in the sense of permanently separated, by whatever means you choose.
