Elrik,
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.
https://en.wikipedia.org/wiki/Hemicrania_continua
If he says you definitely have CH and prescribed Indomethacin then he's not done his research.
J