Oh man, you must be my twin!
I just, JUST posted a few days ago about this on several of my ball pythons. While I don't know what is causing it, and no one else seemed to either (though low humidity was suspected), I can assure you that underneath the missing scales, he/she will grow healthy, beautiful new ones for their next shed.
You should go find my thread, or I can PM you a link, and see if it sounds/looks the same (I think I posted pics too).
Don't fret! Your snakey will be ok.
2.3 normal ball pythons
.1 ultramel motley het caramel corn snake
1. butter motley het caramel+stripe corn snake
1. fiance I had to rehome my kitty, and my dog got cancer and we put her down. RIP.(Did I forget anything??)