Aftermarket fender flares

Maybe try coating the fender flares with a bed liner product? Any aftermarket flares are just going to get scratched just like your stock fenders did. Would also be easy to touch up.

Raptor liner is supposedly UV resistant (so it won't fade over time), wouldn't look much different than stock Off Road flares.

Edit: Just noticed you don't have flares to begin with on an SR. I would touch up those scratches as best you can, and add whatever flares you want on top. I'd still consider the bed liner route if this is going to be a common occurrence for the wheeling that you do.

 

You won't like the way 4th gen looks then. No more skinny ridgeline fender flares like 3rd.
I like bigger flares. looks like a real truck.

 

I got ya. I was just thinking about alternative options for you, that way you wouldn't have to. It would also make replacement much easier and look cleaner.