1. Let it be, if it’s not too visible. Yes, it perhaps hurts at the beginning. But the case is made for protecting the movement. It’s natural that it will get scratches and dents.
2. If you can’t stand it: try it with laser treatment.
I got a very remarkable, very visible cut in my new DD40 just a few days after buying. It was on the side of the case (I crashed it against the edge of a wall while rushing from one meeting to the other). The watchmaker of my AD did a fabulous job. Even with a magnifying glass I’m not able to find the place, where the cut has been. And the form of the case has kept untouched.
Best, Thomas