Her FP+'s are linked to her park ticket on
MDE, not the resort reservation. Staying at the resort affects the timing only, AFAIK. Once you are past the 30 days, she will not lose her FP+ just because you take her off the resort reservation. She has a legitimate right to those FP+'s at that time.
To be sure: Don't remove her from the reservation until you arrive. Also take a printout of all the FP+ booked prior to going. (I do this all the time as a backup anyway. I just don't trust technology. Guess I'm too old! LOL!) Perhaps, they can leave her name on the reservation with a note attached to remove the extra charges at the end of her stay.
When you get to the resort, explain the situation to them. Double check that she will retain her FP+'s even if the extra fee is temporarily removed from the reservation. If they suggest it as a problem, ask them for a solution. You do not have to pay extra for the nights that she is not there.
It is all perfectly legitimate and should be fine. I have done this myself. It wasn't a problem for us, so, unless something has changed recently, I can't see how it would be a problem now.
ETA: If you are too worried, you can always just pay the extra person fee for the first nights. It can be worth $30 for peace of mind. However, there is no way you should have to pay for the last night after she leaves. Another thing that you could do is book three separate reservations and have them linked. However, that would be a whole lot more trouble and you may have to move rooms twice, So I wouldn't recommend it.