Are there places for your fish to hide in your pond? We have one chubby fantail who disappears about once a year. As soon as we are sure she's gone for good this time, she reappears. I'm talking WEEKS of being MIA. We have no idea where she goes (I suspect she finds her way between the rocks in the walls) but she keeps coming back! Maybe your fish got spooked from being handled and went to find a hiding place... just a thought!