I hate separating a bird, I think it causes more trouble than is fixes. I like to have my broody hens right in the middle of the flock. I have two setting on two different nests as I write. One to hatch tomorrow, I can hardly wait, and one just got settled a couple of day ago.
As for your problem, a few questions for clarification. How many nests do you have? What size of nests are they?
Sometimes, you can create a nest, complete with fertilized eggs, and trap a chicken on there for a couple of days if she is broody, and she will accept this new nest. Sometimes she will accept it for a week and then leave. Moving a broody hen can work, but it can also fail. I have used a broody hen for the last 7 years to hatch and raise chicks, and I leave them in the nest they pick. This time I had to create a new nest for the layers, who are not so picky.
You might decide which hen is most apt to win the fight, let her have the eggs, and break the broodyness of the other hen. How I would do that, is to take the less dominant hen, dip her legs and belly in cool water, then put her in a wire cage with no bedding, just food and water. Sometimes, you might have to dip her two days, let her dry in the cage and by the 3rd or 4th day, she should be over it.
Do mark your eggs with a marker. Every 4 days, go down with a towel, cover the broody's head and pull her carefully off the nest. Be careful of her wings, sometimes she will tuck an egg up there. Put her out in the run, and check the clutch of eggs to make sure there are no added eggs. Keep checking her to make sure she gets back on the right nest.
Good luck, this is the LONGEST 21 days ever!
Mrs K