It is written into my son's IEP that he has a medical condition that may cause excessive absences. When he has been hospitalized in the past and had to miss school, the makeup work was coordinated through the health office, not the special ed office and required a note from his doctor verifying the need to miss school.

Perhaps what they are saying is that makeup work needs to be coordinated through attendance and not special ed? If they're making it difficult for him to make up the work altogether, I'd definitely pursue this until I had something in writing protecting my child.