Some of the links on this forum allow SMF, at no cost to you, to earn a small commission when you click through and make a purchase. Let me know if you have any questions about this.
What I've done with some grills I had in the past that did the same thing, was bush off the flaking paint area with a wire brush, then wipe down the whole area with olive or vegtable oil. It kept the area from flaking again and kept it from rusting. I've never liked spray painting the inside of my cooking area, but I'm sure if you do it right, it would be okay.