Since he is on an IEP, he should have provisions and services for the time he misses due to a medical condition. Additionally, all kids on an IEP plan are covered by section 504.
Here are some links that may help:
http://www.childrenwithdiabetes.com/d_0q_600.htm (this is from a diabetes website, but the issue is the same - medical disability that results in excessive absences)
http://www.acor.org/ped-onc/cfissues/backtoschool/iep.html (this is from a website about kids with cancer, but again the same issue)
Additionally, you should call an IEP meeting and include the following as an accommodation:
(CHILD) shall not be penalized for absences required for medical appointments and/or for illness. The parent will provide documentation from the treating health care professional if otherwise required by school policy.
If the school will not include this in the IEP, I would reject the IEP, and begin the legal process. In my state this could include a facilitated IEP meeting, mediation or onto the hearing process which usually requires a lawyer. But, the law is clear - if the absences are due to the medical condition/learning disability, the school must accommodate him. At the least this means not penalizing for the absence and it could even mean extended school year to make up missed work.
