First off, most water conditioners react pretty much instantaneously with chlorine. With chloramine, which is what I have to treat for, products such as Prime and/or Safe also react pretty much instantaneously. I know this because I have tested many times over the years, using numerous water conditioning products. As I'm sure that
duanes
has. Duane also worked at a water treatment plant as a microbiologist, so his testing methods were probably a lot more advanced than mine.
By leaving the filters running ( I have 3 AC 110's on the 6 ft tanks that I currently have running) the mixing of water, and water conditioner, is mixed in a very swift and effective manner. No bacteria is killed in this process, at least not enough that it has ever registered with regards to water quality, free ammonia, etc. So perhaps some on rocks, wood, substrate, but my bio material in the filters, nothing, or next to it.
Also, if I forget to add water conditioner in my tanks, with 80-90% water change, and approx. 2 ppm chloramine, killing the bio-bacteria would be the least of my worries. Lots of years under my belt, and I have never forgot to add water conditioner, because where I live that would = dead fish.