I think you're too pessimistic about the long term prospects of an Edo-like civilization. The Japanese had an extremely advanced waste recycling system (farmers would bid on the contents of urban outhouses to use as fertilizer for their fields) that maintained or even increased their fertility. Combined with harvesting nutrients from the sea (seaweed, oysters, fish) and using the waste products as fertilizers, you prevent losses of soil fertility almost completely. See the book Just Enough for a more in-depth description of this system. Now such practices require constant attention to detail and to the cycles of the natural world, and may fail in practice because of human nature, but there is hope.