This has happened multiple times as I have died and my item magically dissapears permanently. For instance I died in my own house to a mob that went through my teleporter, I was able to recover most items but my looting 3 sword was lost, I checked my nearby surroundings and mined some blocks to try and find it but it had dissapeared. Another instance is when I removed a doc from the jukebox, it never showed the disc being taken out and had just dissapeared. The same thing happened with another disc but fortunately I was able to recover it. It had somehow went into the underneath block.