BS, I am not sure I follow you. You are postulating that bacteria cannot metabolize NH4, but only NH3?? Although it is true that only un-ionized particles can cross the cell membrane without active transport, it does not follow that the bacteria cannot take in NH4+.
The proportion of NH3 to NH4 is fixed based on pH.
NH3 + H+ <-> NH4+
This reaction is reversible & governed by the Ka of ammonia.
As the NH3 is taken up by the bacteria, some of the NH4 is going to be converted to NH3 (to maintain this fixed ratio), which in turn gets taking up by bacteria. The end effect is that the bacteria will (& do) consume NH4. <This is the main mechanism why ammonia bounded by Prime or other dechlor is still available to the biofilter & will be metabolized. To proof this, measure the ammonia level with a Nessler test after you dechlorinated water with chloramines .... The measured NH4 will drop to zero in a mature tank after a few hours.>
So, no, I don't think this has anything to do with changing pH or buffering capacity. Something is killing off the biofilter & the tank is experincing a mini-cycle. <That something could be very low pH ... say 5 or less .... but I would expect that fish would be stressed if not killed with that kind of pH crash. More likely cause would be soap, chlorine, meds or other things introduced into the tank.>