Since you said you're not sure what type of doll he is I assume you didn't acquire him "new" as originally packaged. If he is a Yogurtini, it appears the gimmick with these dolls was that they were scented and came in yogurt cup like containers. So with this scene feature I can't be certain what that was, whether is was an exterior coating or a chemical mixed into the body or what exactly.
http://newtoybrands.co.uk/yogurtinis/yogurtinis/I know very little about these dolls and what they are made of or how they are made, so my recommendations are rather generic. If your interest is only removing the original scratch and restoring the color, then continue with the sanding, moving up to the P2000. At that point if the sanding scratches haven't diminished enough you may have to move up to polishing with a buffing wheel. Also be careful with the sanding and work slowly. Does the doll feel like it is a hollow skin or solid? If it is a skin, you can't be sure how much wall thickness you have to work with.
Then work to restore the color as
Zirconmermaid suggests.