There is an ammonia issue that Old Fish Lady explained in a thread in the Bowls and Habitats section. I wish I could find it for you. Maybe someone knows.
It has to do with ammonia being held as ammonium by the low pH caused by waste and respiration and the high CO2 that causes. When you outgas the CO2 and start adding higher pH water, the ammonium changes back to ammonia almost instantly. This spike can cause problems. She recommended putting Prime in the cup before acclimating.
This is a perfunctory and not entirely accurate explanation. I hope someone will clarify. Maybe we or you can find OFL's post. I'll look.