MOP cannot really be repaired, but they can replace the stone. But MOP is not that soft. Did you really scratch it or are you just worried you will scratch it? I own a lot of pearl jewlery, and it's pretty tough. I have also dropped my MOP 20 motif, my pearl strands, whacked my bracelets accidentally... you name it.
As for metal polishing, yes, VCA will do that (except guiloche). But do not over polish. I am sure VCA will also tell you this if you keep bringing it in to be polished. When you "polish" gold, you are really removing metal, albeit very tiny. Over time, you will lose that "crispness" in the design because you keep polishing it over and over again (e.g. removing metal and wearing it down). But a good VCA SA will not let you keep polishing your piece.
On WG, if it turns yellow, VCA will replate it for you. I spoke to my SA about this a while ago (I'm a white metal gal), and he said he has never had a piece turn yellow on him. Maybe some of the older vintage pieces. If your piece happens to turn, yes, they will replate. Is it turning yellow or are you just worried it will turn yellow?
Unless your piece is really banged up, I would not obssess over a few dings. It's jewelry, you will get dings. I look at my dings as jewelry that has been with me through my journey of life. My watch is also another one that gets banged around a lot (I currently wear a SS Daytona), and I have never buffed it out. I did that with my very first Rolex and regretted it.
Wear your bling and enjoy it!
