yes they will as some1 had his front calipers replaced for this reason! take it to the dealers and get it sorted
You called, it was me and i'm gonna get the rears in shortly as well
My front AP's had turned pink
and now there all shiney red again
Tell the dealer and he will take photos of them and send to SEAT. remember to mention the paint warranty and the fact that they are painted and therefore covered by said warranty. Be polite and don't take no for an answer.
Just check the state of your pads and disk before you take it in so that they can't charge you for things that don't need doing.
Good luck!