This is the first I've heard about particular things missing from chests. If it's just food I would suggest you're either looking in the wrong chests OR your friend got hungry and hasn't replaced what they took.

If you're running mods, that would be the first thing I would check to make sure they are running ok after the recent updates, especially if you've got a mod which makes food that is not native game stuff.

Not saying it's not possible, just highly unlikely.