I have had multiple occasions where my shulker storage boxes in my inventory completely disappear. It usually happens when it’s not in my hot bar or when I save and quit the world. I was playing I multiplayer and have not noticed it in single player yet.
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Arisa Bot
Thank you for your report!
We're tracking this issue in MCPE-62944, so this ticket is being resolved and linked as a duplicate.
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This has also happened to me several times, just now I lost a shulker box containing enchanted books that I was saving, which led me to look for the issue in the bug tracker. The shulker box was also in my inventory when it disappeared.