I've lost entire chests before (unsecured, outdoors, monster must have gotten) but never specific items from INSIDE chests.

I do have a bad tendency to "I'm going to store this here temporarily" and then completely forget about it.

I have also had the opposite happen, one time playing on a dedicated server, I removed a bunch of items from a chest to my inventory, the server crashed and rolled back to a time before I took the items. I still had the items in inventory and now they were back in the chest!