I don't think I've really ever seen them in the Shallows to begin with. My base is in the Shallows close to the Kelp Forests so if and when I go there I see plenty.
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I'm fairly certain it was only after I journeyed to the Floating Island. I had saved up resources to use for my base but went for the multipurpose room blueprint. I came back and the boxes I placed under my lifepod were gone. …
Late update, but what I ended up doing was using the teleport command to get outside the Aurora. I hadn't previously used it so I didn't know exactly where it would take me, but I ended up right by where I parked my Sea Moth, none worse for wear. Th…