Thanks! I have a pretty solid grasp on the chemistry of fish tanks and I don’t think bacteria are free swimmers. This is also quite evident when I do the large water changes, as the rate at wich the bacteria still break down ammonia and nitrite seems the same.
Even though I am not concerned for the bacteria as such, and actually not at all concerned for the nitrogen cycle at large, there might be other circumstances with fresh water that may be affecting the most sensitive of the fish. I am considering apilitting the tanks into hardy and sensitive fish and experimenting with smaller and more frequent water changes for the sensitive ones.