I have one that had Hole In The Head 3 times, who scratches his head frequently on his house. I believe this is just the healing tissue. If the piranha has this, it will eventually deteriorate it's face to fatal conditions.
I have noticed, however, there have been times after the disease where scales are missing from his forehead as well as random gouges - This I believe to be caused by the piranha 'spooking' and crashing into tank equipment, as they are very skittish by nature. This could be a possibility.