This happens with decentralized farms, too. The problem is not in the kind of farm, but with the techniques used. Tractor tillage increases yields, but is hell on topsoil.
[1] https://www.scientificamerican.com/article/only-60-years-of-...
If you're drawing on the aquifer faster then it replenishes, it'll eventually run out. Sure, it'll replenish itself - eventually - but the land you were cultivating will be unusable for decades. In the meantime, all of your nice topsoil will turn to dust, and blow away.
It's easier to conserve the soil that's already there than to make new soil. That said, there are techniques to increase the production rate of soil. Sheet mulching can create 4 inches of topsoil out of waste organic matter in 2-5 years (compared to thousands of years for natural processes).
Generally it's better to make soil "in place" because moving it breaks up important soil structures, leading to oxidization and nutrient loss.
https://en.wikipedia.org/wiki/Sheet_mulching
http://tobyhemenway.com/resources/how-to-the-ultimate-bomb-p...
"Damn nuclear apocalypse, it's been weeks since I had fresh basil! How can I feed my militia if I can't even bake a pizza?"
And even before we get to that point, a distributed agricultural system would help lessen our reliance on large-scale industrial farming operations which we are frankly not using at a sustainable (1,000+ years) rate.