When manure is on the floor, you can hear the flies surrounding it. I placed some manure on the floor of my house like a neanderthal and, even though I have picked it up, the flies can still be heard. When I walk to the other side of the house, it's much quieter, suggesting the game still thinks the manure is just where I left it.
This also extends to other inside areas, like other houses and dungeons. I can still hear the flies buzzing even though no manure is to be seen.
Put manure down in house, pick it up