Unfortunately, that's something that I've had to deal with too. When I was in school I made sure to always keep up with my work and only miss if I absolutely HAD to. We tried our best to work out all doctor's appointments to be on my days off, but it wasn't always possible. The worst was when I would get bronchitus and be out for a month at a time. Even though my mom always picked up my work and I kept up with it, I was told I had to make up the days at Saturday school when I finally came back. Not that I had anything to DO there, I'd already made up all of the work. Unfortunately, that was the school's policy and there wasn't much we could do about it (though my mom was able to get them to reduce the number of Saturdays they made me come in).
I think the absolute WORST, though, was the time that I was out for bronchitus and my mom asked all of my teachers for my work and my health teacher told her I didn't need to worry about it for her class. And she gave me a 70! I had been an A/B student all my life and would have had an A in that class if she had given me the work to be able to do it, but SHE didn't want to be put out and get the work together for me, and punished me for it... Grrr!
(here it is 15 years later and it still gets me mad)
Now, I happen to be a teacher, and ALWAYS work with my students that I know are out for legitimate reasons. Unfortunately, the policies are put into place because there are some students who will miss a lot of school for a slight sniffle or because they stayed up too late the night before and DON'T do the makeup work. I would suggest talking to the individual teachers and see if they can work something out. Especially for the classes that she has actually been present in most days. Most teachers, you'll find, are pretty caring if you approach them the right way. Don't go in accusing them of being unfair to your child. Instead, ask them if they could explain the policy to you, because you are somewhat confused as to why she has to take the exams in classes she has been there for... It's a thought anyway.
Wish I had a better answer for you! Good luck to you and your daughter. I can completely sympathise.