I already posted something about this. V.W anti corrosion warranty usually requires you to have the car serviced and inspected by them when they can try and catch this problem early (unlikely). V.W will define what they mean by 'corrosion' and are unlikely to compensate when the paint starts to bubble when it's all too late. IMHO even with a fully maintained EOS, I wouldn't expect anything beyond 10 years? If you were offered anything now, they might give you some goodwill and you pay the labor. But a pair of new aftermarket fenders fitted and painted in a non-V.W shop could be a lot cheaper?
If you search the auction sites you may find sellers selling new front Fenders (Wings) for the EOS. They are bolt on, no welding and not too hard to fit DIY after the front bumper and grill is removed. Mine were of Tiawan origin (?) and cost about £95 each compared to circa £250+ from the stealer. I assume they were patterns and I had very few problems getting them aligned with correct shut lines. By the time a body shop has tried to repair, fill, and repair your fenders it will probably cost more than replacing and repainting them and you will see the repair. Later on you will get the rot somewhere else.
This is why your fenders have rotted: Inside the top arch of the fender behind the plastic cover, and vertically down the inside near the door hinges V.W use a thick wadge of their famous water absorbing 'open cell' gray foam which sits in contact with the metal fender. You can't see the corrosion progressing and it usually shows first along the top center line of the fender. The foam is used to reduce some of the tire noise.
If you bite the bullet and replace both with new, you can get the painter to add coats of anti-stone chip paint to the inside of each before painting the outside. And of course you remove and trash their nasty foam. You will hardly notice any change in cabin noise level.
