jamie,
Yes, you are experiencing a die-off (Herxheimer's Response). Fungus, not bacteria is being killed because you are starving it by reducing foods that feed it, along with taking the Nystatin, a powerful antifungal. That is a good sign, actually. You know now that you have a fungal/yeast problem. CD and UC has been known to have a fungal etiology. I'm betting your CD symptoms will lessen as you continue on the antifungal program.I would stay off the potatoes, and all grains, as well, for awhile. They are high in carbs/starch. Check the sugar content in the Ensure. For me, I had UC symptoms, on and off for 8 years. After following an antifungal program, with natural antifungals, I was well within 2 weeks. I did experience the die-off as you described. I thought at one point I was going to have to go to the ER, I had severe joint and stomach pain, LOTS of D, and very tired and foggy brained. Stayed in bed for a few days. After 5 days, I was on the road to recovery. Good for your doctor to try something like this. Many doctors don't know, or believe that fungus can cause many of our health problems. Let us know how you make out. :)
Kim