In the game i am currently playing, i took over a kingdom city with a great mill in it. In order to deal with my subsequent population catastrophe i had to demolish most of the building in this town, including the great mill since i already had one.
I took one of the food production cites a few turns later which brought be back to a population surpluss and i discovered i could build the great mill again. Even more crazy, i'm building it in the same town with my first great mill, so we will see what happens when it completes, but i don't see anything happening right now to prevent the double bonus. 
maybe the ai is trying to drown me with bricks.
I'm glad we got rid of the "you built it once now you can't ever again now its been destroyed",
maybe if i find a gold mine i'll move my lv 5 city there and rebuild the mint of revenna which kinda seems just wrong...