What does your employment agreement with her state? Is the contract subject to renegotiation at any time? Is the % fixed or varied? Are you willing to lose her (entirely, or even dropping her to part time) if she quits because she's losing $ and % for the decrease in responsibility? Is this dictated by the franchise agreement at all, or these are you own hiring practices/standards/rates (which I'm sure are competitive in the field)?
To answer the question, if the bonus is "based on growth in revenue" and she's not making much in Territory B, won't her $ and % go up if she's exclusively working Territory A? She won't have Territory B dragging down her #s.
I guess if she has less responsibility, you could decrease the amount of bonus... but at what cost to your business as a whole?
I love her and don't want to lose our demote her. I'm leaning towards keeping her original bonus the same, bar her bonus on the one territory but set get goal and a slightly larger growth target since she is only putting her efforts in one area. Also I would want he to help me hire so she feels like this person is there to help not hurt her.