I think the OP is referring to the tissue bubble on the topmost head(s). That's not a barnacle. And I've never seen my hammer do that when it split heads...
While I haven't seen anything like that happen to my hammer, I have seen it happen with two different brain-worm corals (platygyras) in spots where thin skeletal growth beneath allowed small areas of flesh to detach and form bubbles. They never spread and would inflate/deflate regularly depending on the strength of the current. Eventually one of the two 'popped' and then the tissue reattached itself to the underlying skeleton.
I don't know what it is - maybe someone else will chime in with some other ideas...
For now though, if it were me, I'd just leave it be.