These are typical of the problems you get with running a sand base and why I prefer gravel with no vacuuming. In this system the whole base becomes inert so you are relying solely on the filter, that can be dangerous if the filter fails.
Typically most gravel or sand substrates are inert.
But this makes little difference as bacteria will grow fine those surfaces anyway, just that sand has less surface area is all.
And vacuuming substrate wonāt remove the bacterias anyhow has these BB are pretty much glued on surfaces with their protective clear coating.
In fact inert substrate is in many ways better for keepers as this helps maintain water parameters and avoids pH swings and suchlike.
The only substrate I donāt like is super fine sand or fine silica sand as this tends to lock or compacts tight making it harder for plants to grow and also surface of super fine sand can be stirred up easily by livestock.
But in reality most fish keepers use substrates that are inert anyway and I doubt this has much, if any, impact on the OPs ammonia level at all as bacterias will form on pretty much any surface on substrates.
In this case it could well be down to removing the internal filter and adding a new external filter without moving the old media to the new filter to encourage more growth of bacterias inside new filter housing.
Donāt think itās conclusively just this but defintely played a factor in ops ammonia levels imho.