Please go ahead and try the parasite cleanse with zapping. No one here makes any claims for these health protocols, but many people who post here have great things to say about the health changes they have experienced.
It does kill the bacteria to some degree that are near the intestinal wall, but also kills the bad bacteria. What tends to happen then is the good bateria flourishes in their less hostile environment. And you can always take some probiotics to colonise you system whith a healthy flora of bacteria.