Ok, it would appear that if you stop a building during production you simply lose any resources it took from the storehouse to use i.e. when you restart production the building doesn't continue where it left off, the settler immediately goes back into the storehouse and picks up a fresh set of resources.
That been said, is there any way to prevent this? Perhaps it's a timing thing, you know, if you stop EXACTLY the second the settler takes the goods into the storehouse, he'll deliver the goods, but won't pick up the next set of resources and simply stop?
I know it's no big deal, but i've got a gold mine and gold smelter running and i'm only running them buffed, so obviously i'm stopping them all the time when I know I won't be there in six hours. It just annoys me a little to think i'm losing bits of gold here and there!