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 I’m curious as to how it distinguishes between the good and the bad. 
 To be honest not a lot of known about the stuff because nobody's incentivised to study it. There's a lot of people using it to treat a lot of things but I suspect that they don't know a lot about how it actually works.

It's said that it works through a mild oxidation reaction. Human cells are used to using oxygen & so are not effected. Anaerobic microbes & certain defunct cells are not resistant to high oxygen environments. Most of the organisms we consider good are aerobic.

What we know is that it's not like antibiotics that kill indiscriminately. 
 Found the book where I learned about Chlorine Dioxide:

https://educate-yourself.org/cn/Miracle_Mineral_Solution_of_the_21st_Century-Part-1-Archbishop-Jim-Humble-Free-2006-Edition.pdf 
 Haha wow - that's an old one. The Jim Humble stuff put me off when I originally stumbled upon it.  The church that he set up to protect what he was doing felt off to me (I was fairly anti religion at the time).

Andreas Kalcker has picked up when Jim left off. He uses CDS which is a more pure version of chlorine dioxide & is super easy to make at home.