I was on my friend's vanilla minecraft server, and he accidentally shut the server off when I had my "Gear" shulker box in my inventory, which had my elytra. When I logged back in, it was gone from my inventory and I tried clicking in my inventory, walking around to try and pick it up, or checking where it was last, which was my ender chest. I ended up not finding it and I also lost another one of my shulker boxes straight after that, when my friend (the host) left.
The 2nd time I lost a shulker box he did not accidentally turn off the server, he did /save-all and I still lost it.