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It's clearly a bug. My fix was just to create a new one using commands. It's not cheating if it disappeared due to a glitch to do it that way, as far as I'm concerned.
This happened to me twice. I had my Seamoth in my Cyclops, and after sleeping (I'm pretty sure it what triggered it) it disappeared. The Cyclops still thinks its docked, but it isn't. I recorded it as proof. The first time it happened it was fully u…