The nature of removing dents in a burnishing action with a steel ball on the inside of the instrument and a powerful magnet on the outside will almost always results in scratches. The options are to leave the dents in the instrument, or take it apart and see if you can achieve better results by removing them via traditional means. There are means of reducing scratching that technicians have brought to our attention over the years, but we only ever use Mylar sheets with lubrication and do not have a problem with this method. The trick to not scratching silver/lacquer during the MDR operation is to have a large enough piece of Mylar and tape it to the body section/area of the dent. Using this method, the magnet moves over the Mylar and it is not moving over the surface during the operation.
One method that has met with success was originated by Jerry Gilbert: Use a layer or layers of chamois cloth over the end of the magnet(s), secure them in place with a heavy duty rubber band, and soak the chamois with Pledge. Another MDRS user has had some luck with the Blue assembly tape that Allied sells for that small dent that you are going after on a newer horn. Just tape over the dent, lubricate, and proceed with the operation.
You may be able to find interesting discussions on this topic (along with many other repair related topics) on the Delphi Band Instrument Repair Forum. Contact me at email@example.com if you need help accessing the forum.