The chest update affects only chests, those items are not loaded in by the servers like the chests, they come with the map. The server system doesn't know nor care about those items, they are just another interactive block to it. They have to all be removed by hand and the maps saved, which is not an easy job to do, especially because not all the item locations are known. If a furnace or dispenser has a potion, it will remain until someone takes it, and will not restock when chests refill, only when the map is cleaned up (restored to a pre-game state).