I've loaded tens of thousands of .38/.357/.45ACP nickel cases and have not experienced the problem of which you speak. For at least twenty years I have used only carbide dies for handgun cartridges and thus may have "forgotten" about the flaking nickel problem relative to steel dies.
Some folks reload bottlenecked nickel rifle cases without problem--so I don't know what could be causing your problem with scratches. Luck!!!!
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