At this point I try not to sweat it when things like this happen unless it's a big fish in a small tank. Among other mysteries:
-A surprisingly large number of tanks I've moved for people have a fish stuck to the wall behind the tank.
-I've helped people move down tanks, carefully checking each rock for fish as they come out. A surprisingly high percentage of the time we end up rescuing a goby from the floor a few minutes after laying the rocks out.
-When I tore down my tank in DFW I never found my big turbo snail. This guy was at least the size of a baseball, and I'd seen it the week before. I checked every rock and never did find it. The only thing I can think of is that he snuck out on a rock when I was selling my SPS colonies.
-Other than the skeleton taking some time, an established reef tank is amazingly good at reclaiming a dead fish, especially if you have a thriving bristleworm population.
-I had a tomini in my sump/frag system that vanished for a solid year. Now, there was macro down there, a couple frag racks, and some live rock, but I spent a LOT of time looking for him, and a lot of time working in there since it was my frag system. I didn't feed the sump or the coral in it, and there were plenty of unprotected pump inlets. A week before teardown I watched him swim by. He even grew faster than the one I had in the display.
-A lot of clowns and other fish have been found living in small overflows a year after they went missing. Often overflows that don't seem to have openings big enough to permit a fish in.
-I once rescued a 9" long puffer from an overflow on a tank I maintained. The overflow had tiny slots, and a lid zip tied on to it. The lid could lift about 2" in one corner before the zip ties went tight, but there wasn't much excess space to grab the edge and lift. Not only that, but it managed to get back in to the same overflow within a couple days of being pulled out. We ended up having to zip tie the lid on a lot tighter.
Point being, fish are really good at getting unexpected places, they don't always come back out, and it seldom crashes a system.