Bubble tip anemones can strink down to almost nothing and hide in holes, under ledges and so on. The Chromis could have fallen victim to disease or the anemone and the clean up crew quickly did what they are supposed to do, chow down and they do that very quickly.
I imagine the anemone will show up eventually, but probably not the chromis.
Moving rocks around is a futile effort, you'll not likely change the outcome for either the anemone or the chromis. Rationally they can only go so far, so if they are not in the overflow or on the floor then something has eaten them. My advice is to not move around rocks looking for lost tank inhabitants unless you absolutely have to.
Good luck and I hope your anemone shows up soon.