I've built several "well II"s and upgraded them before they got manned... and not, still being unmanned, their resovoir is decreasing... I haven't been able to verify whether the water actually comes into my warehouses, but the wells are definatley unmanned, and water-resovoir is depleting.
This bug seems to be "working" on my mills too, as in, my mills is milling, but again, I haven't been able to verify the activity.