There is a law of preservation of energy. Elements don't transmute into each other, and don't appear out of nowhere.

The mass of biologically available nitrogen, and phosphorus in the harvest is equal to the mass of nitrogen, and phosphorus removed from soil.

No way around this. When there will be no nitrogen, and no phosphorus, there will be no crops. There will be no material for plants to use to make its cells from!

The "Organic agriculture" crowd sound to me very much like antivaxers, except fighting the agriculture industry.

This is simplistic to a fault. Legumes, for example, fix nitrogen; we've known for thousands of years about crop rotation.

Runoff and erosion - processes that tend to be sped up by industrial farming techniques - cause phosphorous depletion in a way not due to the harvest itself, as well.

There are a lot of factors in soil depletion. Some are under our control, via different farming techniques, changes in density, etc.