Yes this will harm him. The carapace will abrade to the bone. You should not place too many abrasive materials in his enclosure. A shell infection is tedious and sometimes fatal. Also, there are shell additives that supposedly benefit carapace and plastron health in Tortoises with things like vitamin E and Keratin (i.e. vitashell). There is a view though, that these types of additives inhibit the proper growth, namely hardening of the growing shell, so use of them is at the owner's discretion.
And tortoise shells don't really shed. The shell of a tortoise grows somewhat like a tree in concentric circles, originating from the centre of the scute. I have never seeen my torts with dead skin flakes on the plastron or the carapace. That being said, I have seen dead skin flakes in my box turtles' shell and also on aquatic turtles when I used to keep them.
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