Lose them. You're changing most of it anyhow so it'll be easy.
Your car is a bright color so I'd take the time to fill the holes in the rockers. If it was dark I'd say screw it but I think it'll be too noticeable not to.
Worst case pop them off and see how it looks from a distance. If you can live with it great.
The rear bumper on my Camaro was off an rs car and still has the holes but you don't see it cause it's black
