CNCReefer, it sounds like you hit the nail on the head when you said a power head pulled it off the skeleton.
What yuor describing sounds like laminar flow damage.
You migh tlook into getting a wavemaker power strip, you simply plug your powerheads into it like a normal power strip, but it has a micro-chip in it that will cause it to turn off and on, causing more chaotic action.
You should also make sure power heads are never pointing directly at invertebrate life.
Another option is a device called a SCWD, which will do the same thing a wavemaker does with ONE power head through gears and plumbing. (I like SCWDS personally)
If you want to upgrade and your tank is big enough, you could also look into getting Tunze streamers. they produce a larger current that doesn't have the concentrated flow of water channeling through the center that can cause coral damage.
As for the brain, keep feeding it, watch your water quality, and hopefully it will produce another skeleton. I have never actually seen or heard of this damage going so far, but here is hoping!