Yes. The AquaMira can cause some loss of various gut bacteria. It promotes other bacteria. Your mouth is slightly basic (well, saliva is.) Your stomach is highly acidic and has a small amount of hydrochloric acid. Bile and other chemicals are released to bring the pH up to near normal in the upper small intestine where it stays more or less. Breakdown often is acidic, so your body releases mucous along the way which is similar to saliva. This back and forth between basic, acidic, basic kills off all bacteria you eat, usually. A few can survive it (of all the thousands out there) and make you sick.
Adding chlorine, CLO2, etc can change the chemical composition slightly, sometimes leading to intestinal problems. I have never heard of stomach problems, but this is possible, I guess. But the stomach is highly acidic, anyway. Chemicals hang around a bit longer through the small intestines and can cause problems in some people. I believe the label on AM says something like “emergency use” or “not for long term use.”
Anyway, I gave up on filters after one froze on a spring trip. I gave up on chemical treatments due to the long wait-times (especially in cold water.) I use UV primary, and, have a few tablets for backup(chemicals) and at night, and, I can boil water if I get really desperate. Good enough for me.
I would note that changing water supply’s can often cause a temporary problem, too. This is about the same as introducing chemicals into the water at the concentrations we are talking about. So, AM/chlorine dioxide/chlorine/iodine is not what I consider unsafe or debilitating. It just takes your gut about 24 hours to catch up and readjust.
Filtering can change the taste by removing a lot of organics from water. UV doesn’t remove anything, nor, kill anything. It merely distrupts the DNA of bactera/viruses. Chemicals can change the taste of water whether it is neutralized or not. Adding any chemical ions to the water can be tasted by many people, but not all. For example, years ago, I used AM drops a lot. My daughter could taste it. I could not. She always needed to use kool-aid to cover the taste.
No methode for water treatment will render all water safe to drink. Water with large amounts of arsenic for example will pass through a filter, and will not be neutralized by chemicals or UV. For example, water contaminated with blue-green algae is often contaminated beyond drinking with the toxins produced by the algae, not the algae themselves. Special filters can remove the toxins, but, anything we use in the back-country cannot. Even the small charcoal filters only remove a small portion of arsnic or mercury, for example. Fertilizers/pesticides, are other toxins that are passed through. You need to be aware of the source whenever you go hiking.