Sometimes spinal manipulation (especially in the neck) can flare autonomic dysfunction if the space in the spinal cord is tight.
This is not a big deal and simply requires a tune up. Begin with taking (or continuing) a nutritional supplementation program that targets CFS. Include Ribose and add natural remedies or medications (Ambien, Desyrel, Klonopin) as needed to get your eight hours sleep a night. Ask your doctor to increase your thyroid dose to see if it helps and if spastic colon or nasal congestion symptoms are present, consider treating for candida. Add in vitamin B6 each day for 6-12 weeks as it can help recovery from the chiropractic manipulation.