i got this answer from another website.. hope this helps..
It does not appear that zapping has any appreciable detrimental effect on the good bacteria that reside in the gut. There is not general agreement about why this is exactly; some theorize that it actually the result of pathogenic bacteria being killed which would result in less competition for the beneficial bacteria. Dr. Clark, the inventor of the zapper, states that the output form the unit does not penetrate into the gut where the beneficial bacteria reside. In practical experience, zapper users do not report the types of intestinal problems that would suggest eradication of the probiotics. For anyone concerned about this or already experiencing digestive problems, I would suggest supplementing with a probiotic.