Kay, I'm thrilled that this blog shed some light on possible reasons for your headaches.

I checked with the EDS care team at Mayo Clinic and Dr. Knight confirms that:
"Osteopathic manipulative therapy (OMT) and manual therapy can be very helpful for a number of conditions related to headaches. Not only muscle strain reducing, but also helpful for certain types of headaches linked to back or neck pain conditions, called “cervicogenic headaches”. Just remember though, as Dr. Rozen pointed out in this post, there are a few other causes that can be contributing. Keep these in mind if OMT is not working. Let your doctor know about your EDS diagnosis, and see if a consultation with a neurologist specializing in headaches may be needed."

Hi @michelle12 and welcome to Mayo Clinic Connect and EDS blog. It sounds like you've had some particularly rough times with the bone flaps and reinfection. This is a situation worthy of further investigation and Mayo Clinic often provides second opinions in complex medical matters such as this. I encourage you to request an appointment with the EDS Specialty Clinic at Mayo Clinic in Florida.

Here's the link to the request an appointment form to get you started. You fill out the form and a Mayo Clinic to arrange a phone call to get more details from you and schedule you with the right specialist, etc. http://mayocl.in/1mtmR63