The OP has received plenty of advice, and I don’t have a lot to add in that area. It feels awful to be treated unfairly, especially if you are an adolescent (or are the parent of same).
I can share what was helpful for me. I took the attitude, that I shared with my kids, that a grade is the teacher’s attempt to guess how well a student has mastered the material. Sometimes they are on the mark. Sometimes they over- or under- estimate. All the teacher can do is find a way to sample knowledge/performance.
What really matters is how much the student is learning. My son (more than my daughter) took risks regarding grading. He knew that he sometimes lucked out (homework wasn’t checked) and other times luck failed him. My daughter was quite compulsive about the details, leaving much less to chance.
I could easily see my son making the same error as the OP’s son. My stance would be a very sympathetic “you gambled and you lost this time.” It sounds as if he did an admirable job of advocating.
I don’t see a problem in sending the teacher an email, copying the department chair, and saying
Dear Ms. So and So
I just wanted you to clarify the policy in your class regarding work missed to illness so that I understand it. My son’s explanation left me with questions. My son …[politely tell your story showing respect for authority, etc]
It’s not accusatory, it’s just a question. It gives her the opportunity to tell you the policy, and having the department chair on the email chain ensures a response.
I would email the teacher and say “My son says this is what happened…(list what happened), but I want to make sure we understand what you communicated to him…as you know sometimes kids don’t always have the whole story”
if you don’t liek what you hear then i would talk to the guidance counselor and ask how this should be handled.
I agree that if it is decided that communication is to be initiated, then you start with the teacher and the teacher only. If you are not getting any response at all from her or if that response seems to violate the make-up policy, then I would copy the guidance counselor or department head on any future correspondence.
Copying someone above her in the first correspondence is in my mind too provocative and does not give her the opportunity to resolve the matter first. She is only going to interpret it as you trying to obtain leverage by going over her head.
Of course I meant after she failed to respond to your initial email.