Many fish engage in this scratching behavior, but I have rarely seen it result in actual damage to the scales. Given the situation as you have described it, I would hit the tank with an antiparasitic med. The only one that I have any experience with is a product made by Jungle Labs which is in the form of a large, effervescent tablet (kind of like a Fizzie). It has no effect upon biofiltration but may cloud the water a bit. As far as your fish healing, my fish are always getting beat up and nicked and these wounds heal completely and undetectably.