Its possible the butterfly was picking on the other clams but I think I would have noticed. I watch the tank pretty closely especially if things aren't doing well. At this point I'm not ruling anything out and I've changed a few of my practices to see if the deaths stop.
I don't recall ever hearing of a butterfly ceasing to eat coral/clams after it has started. Have you? How long have you had yours again? Mine didn't begin to eat aptasia until month 2 and left all of my coral alone for basically the first year.
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