Sand can be inert (not effecting hardness or other parameters) or not, depending on where it was mined, or found.
Because i live in a remote area, and its difficult to get inert, or any commerical sand here, I use beach sand, so it contains the shelfs of long dead mollusks (calcium), and it ellevates my pH to above 8. At certain times of year, I use rain water for water changes which tends to lower the pH, and the rain washes tannins into the outdoor tank. This lowers the tank seasonally to pH 7, but .... to get the pH to significantly drop using only tannins, the water color is tea brown, and ai times I can't see to the back of the tank.
You mentioned a slight ammonia spike.
Removing the substrate may be counter productive, because it may hold a significant population of beneficial bacteria.

What is your normal tap water pH, alkalinity, and hardness?
These parameters will tell you what you are dealing with, and "maybe" how to proceed.
Medication may also "not" be what is required, and throwing meds at a mystery problem counterproductive.
There could be many causes, it may just be your parameters, and the breeders water parameters may be very different.