I've probably seen worse and made it right again. I did have to replace EVERYTHING electronic, pull the interior out of the car to dry it, clean it, and treat it, then replace a few parts. To keep it correct as a Special Edition will be difficult if the leather is damaged, but parts come up for sale from time to time. If you are paying a dealership do the work, you would probably be better off buying another car.
My 'flood car':
http://986forum.com/forums/show-tell-gallery/70709-houston-04-se.html