Ripe, my opinion is that you should allow STBXW to have the "make up" day. It's not her fault she was sick (you handled that whole thing nicely, BTW), and she does need time with the kids. I would also gently make sure that S9 knows you while you want to hear and value his opinion, the two adults will make the final decision, and this time there was a good reason for the change.
Child sharing is one of the things STBX and I do pretty well. We have a schedule (he gets 5 of 14 overnights), and we are both flexible with it when needed. If he has business travel on one of his nights, I always take D12, and I always offer him a make up day. Sometimes he takes it, sometimes he doesn't. Last week he had to miss a day, he declined a make up day, so I invited him to dinner Sunday night so he could spend time with her. It works for us.