Any method to remove the scratches would involve removing steel from the front of the cylinder. If they are not deep, and your gun is on the low end of the cylinder gap spec. You could polish them out with some fine grit sand paper. Keeping in mind that doing so would be widening the cylinder gap.
My most shot gun is a 686. It has and untold number of rounds fired through it since I bought it new back in the late 90s. My gun is still within specs, and still shoots as well as it did new. That said, I was bothered enough by the notch peening that I bought a brand new cylinder.
If the scratches bother you enough, a new cylinder is always in option. It would require some fitting though.