OP, give him a mental health day tomorrow. Just don't make any connection between his relucatnce to go to school and taking a day off - so as not to set up any expectations for repeats of those days off. Tell him that if he wants to work on school stuff with you (in your office or otherwise) he can do so for a change just this once. If you decide to repeat it at a later date, just do so and pretend it is spontaneous so that he does not connect it with issues going on at school or his sensitivity.
When I am working crazy hours and feel that my DS is not getting much time with me, I do take a day off and make a field trip and lunch outing out of the day. I tell the teacher that I am taking him out of school to go on a field trip because he is in a private school and DS meets and exceed attendenace requirements all the time. Teachers have always been appreciative of it and have remarked that my DS was happier than usual after such trips.
