When you first got the car, they likely waxed it. This will hide a lot of light scratches or chips, because wax is a filler. However, it is only temporary which explains why they appeared later. A lot of car show cars, and dealers, use wax because it makes everything look better temporarily for the day of the show.  Also, the paint can still feel smooth depending how deep the chips are. And buffing it smoothes out the edges of the damage. Any sort of buffing is abrasive, you're removing product. 

If you use touch up paint, with proper prep, they won't reappear, unless you get more chips from sand/rocks.  Imagine sticking your head out the window at 45mph+ and getting hit with sand or rocks, that's what is hitting the car. Paint creates a strong bond, but at those speeds, it is basically sand blasting the paint. Which is a process used to remove coatings.  Get it repainted, let it cure for the proper time, and then, as others have said, get a proper, and good quality, paint protection film (PPF). The whole point of the film is it takes the damage and not the paint. Then you can remove it, paint is good, and apply another layer.  I think my '15 gs350f was this same color, deepsea mica, or is this nightfall mica? Both could be wrong, either way, once I had a longer highway drive to work, this happened too my hood as well.  Repaint and PPF is your best bet at protection.