So it seems that dungeon chests and minecart chests and nether fortress chests don't refill. There are also mansion chests and end-city chests, but I'm not sure if they refill or not. All the chests give the message that they are unbreakable because they will refill at some point. As far as I know, the minecart chests were the last working (refilling) chests, but now they aren't working either.
The only time you will find loot in a loot chest is when it's your first time opening it. These chests do not refill for the same person again. The system is setup so that the chests only refill for new players who find them.
Are you sure they actually refilled and weren't manually filled or something? Most players I know simply slash the minecart and pick everything up: cart + chest + goodies
They would refill with the standard minecart loot. If someone left some other stuff in the chest, it would still be there in addition to the newly refilled loot. But the thing is now, that no chests in the game refill even if you weren't the one who emptied them. I sometimes come across chests in dungeons or fortresses or villages and find them empty. Shouldn't they be full if it's the first time I ever open them? Isn't that the point of making them unbreakable?
You haven't specified the world you are encountering the issue, so I'm assuming it is Wastelands, as that is the only world with auto-refilled chests. If players add their items to the chest that counts as refillable, the system loot should actually overwrite their items. Maybe this post by Aikar can give some insight?
as said, chests only replenish in the wastelands. and also as said in my quoted post, there is a time delay too. if another player recently looted that chest, it can take 3 to 14 days before the next player will cause it to replenish. as for the belongings warning. I make no promises in how vanilla logic treats items in the chest is why I mention that. From my observation, it will not overwrite your items, but mojang could change that in the future.
