I have two Goniopora frags next to a frag of Alveopora and they are doing great. I have ready that they are in the same family and should be find next to eachother. I can only tell you what I have seen and mine are doing great.
In most cases, if you notice them closing their polyps, this would be a sign that they are not happy next to each other and you should move them. As far as the damage being permanent, I don't think that is the case, but I could be wrong.
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