I'm unsure if your doc doesn't know what he's doing or he's trying an experiment on you. Indomethacin doesn't work on CH. That's not opinion, just fact. It does work on a similar condition called Hemicrania Continua. Some doctors use a short script to see which condition the patient has. If it works you don't have CH. If it doesn't work, then likely it is CH.
If he says you definitely have CH and prescribed Indomethacin then he's not done his research.