A lot depends on the number of birds all together, the health of the birds, and the space and how it is set up.
If I read your post right, your flock will stay together in the half that she has for new chicks? Does that have its own run?
Disease is a real possibility, people have lost whole flocks, but if they look pretty healthy, and yours are pretty healthy, it would not be a game changer for me, but it is a real risk.
Moving them in the night, often times helps. If you are combining them with her flock, then hideouts, and multiple feeders help. But while chickens hate change, they do tend to get over it and adjust. They may go off laying for a day or too, but should be fine.
Mrs K