It doesn’t leave earth, but commercial farming practices lets all those nutrients run-off to pollute the water systems instead of being retained in the soil. Where they end up is difficult to recover.

Furthermore, soil needs to be alive, and commercial farming practices kills it every year. So instead of building up soil fertility year after year, external inputs is added year after year in a self-destructive cycle.

See my other comment about CO2, with enough energy all things are possible.

There is something called the "phosphorous cycle" but its a lot like oil and does not replenish anywhere near the rate we consume it.