Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
There is a pretty good population of nitrifying bacteria in the upper areas of the substrate. They need oxygen and ammonia, which means good water movement. There just is not that good water flow deeper down.
Your current substrate is pretty shallow, but even so, I would be surprised if there is a significant bacteria population any more than 1/2" deep in a coarse sand. If yours is a fine sand, then even shallower.
If it is a coarse sand, and you want to save the bacteria, then carefully skim the top 1/4" of sand and place it in several nylon stockings. Then remove the rest of the sand, and remnants of fertilizer tablets.
Hang the nylon stockings of sand in an area of good water flow. Once a week remove one. This spreads out the loss of the bacteria over several weeks or longer (however many bags of sand you have set up, or until you get tired looking at them).
That is a most conservative way of doing things.
I would do as you plan: Move the fish and any decorations, current plants and the established filter to a spare tank.
New substrate, plants into the main tank, then move the filter and the fish back.
The new plants will probably take the place of whatever bacteria you are losing.