I think when ever we are sick enough to study health and take natural remedies we are often sick with multiple infections causing imbalances in our bodies. When we kill off one infection then we can gt alot more symptoms from a different infection. Others might handle these infections/parasites but at this point our immune system is messed up and so we are vulnerable. At this point it is do you suffer and continue treatment for the original infection or add treatment in for the second infection.
I have had success with bloating using digestive enzymes and if that doesn't work then I go to collidial silver. If it were me I would get a natural doc who can tell me what infection is coming up next and add treatment if I can tolerate it. He would also be able to help build up your immune system. I would only see a practitioner that has a way of reading the body, like Kinesiology or acupuncture.
I think so often we are treating for the wrong thing or for one of many things when we could be treating for more than one with info. All these things are reproducing all the while. Its worth it to get an accurate read from a professional. Herxeimer exists, but its too easy to call it a herx. What you are describing does not fit the original theorists definition of herxing, whihc is flu like symptoms.