If it's too deep to polish out, then your choice is either touch-up paint or repainting the entire bag lid. I use touch-up paint, a lot of touch-up paint. It doesn't look as good as new, but it's OK.
Stickers work for small but deep scratches which won't buff out. Alex sells those reflective stickers that I have used in the past (but not to cover scratches).
For rash or larger scratches/damage - Garauld does most excellent work - Good as new!
My right bag decided to slip out of my hands when I took it down from storage in the garage rafters and bounced like a basket ball into the driveway about 20 feet away. It was not pretty. I was so late for work, I just slammed it on the bike and took off. But- she has some major scratches.