I think all of mine, at some point, have done something like that. I've always treated it with arnica gel and pellets, and left it alone. We joked that my 3rd child needed a padded helmet, she was so prone to knocking her head on hard objects.
Seriously, does your child seem to be bothered, or to be in any way damaged (beyond cosmetic) by the bump on his head? If not, the indent will probably fade with time, and I would leave it alone.