I'm guessing that ozone must work in a similar manner as other things that kill bacteria such as garlic or stomach acids. Some clever researchers set up a model of the human gastrointestinal system and put yogurt through it. The stomach acids appeared to kill some of the good bacteria in the yogurt, but later on in the digestive system, it came back to life.
Someone else tested garlic on a variety of bacterial foods and substances like yogurt and they said garlic kills everything, but I would imagine, as Hveragerthi writes, enough of the good bacteria survive (and no doubt some bad, too), that if the system is hospitable to the good bacteria, it will proliferate.
I would also imagine if a person keeps the old ways of eating and thinking, his or her system will be more hospitable to the bad bacteria and it will proliferate again as well and the illness/disease will return.
I believe that pharmaceutical Antibiotics do such a number on good bacteria that it is difficult to regain the correct balance. I feel like I've been struggling with this most of my life since doctors put me on Antibiotics .