Tough as it is, you are going to have to sit down and have an honest conversation with Mom.

You are going to have to be really clear that in a group care environment, the children are expected to conform with the routine, the routine cannot be changed based on one child's needs.

Ask her outright if your routine suits her or not. If it doesn't then she can hand in her notice but it if does, she must respect that you are not a nanny working exclusively for her family but a group care provider. While of course the individuality of a child is encouraged, her child is just one part of a group and unity in the schedule is paramount. Tell her to let you know within a week if she's in or out.