Enderchests that are stored in the inventory disappear. The first time it happened, I thought I misplaced the Enderchest somewhere. After this, I crafted 4 enderchests thinking, if I misplace it again, I have 3 more. However when played on my survival world today, the 4 enderchests disappeared. No other items have vanished and enderchests placed on the world work normal as far as I know. Items placed inside stay intact too.