I'm not sure about the refractory headaches, but is it possible that the Topomax was helping your son more than he thought and without it they are getting worse again? I've noticed that if the migraines get better really slowly it's easy to not notice it until you take away whatever medication that was helping.
Hoping your son feels better soon,
Dx: Chronic Daily Migraines & Chronic Depression
PRN meds: Tylonal #3 and Tramadol