HMmmm good question. ITs probably one of those things that is very unlikely to happen. But You can still get your car serviced and everything as long as you have a cam cover on there. But if your engine blows you could just put the stock cams on there and be like I dunno. Just make sure you dont have any other mods on the car including stickers. Also never put other mods on the car and take it into your ford dealer. THey will take down a list of what you got on your car.
here is a little bit of info, correct me if i am wrong but the last time i checked Crane makes the stock cams for the car and there fore stamps the ford logo onto the cams. Now i know that on the after market Crane cams Stage 1-3 they have stamped the ford logo onto all of them making it harder to find out if they are stock if you took it to a dealer, unless they take the gear off and see the model number on the end of it.
i have cams in my car and have never had a problem with warranty, and ive been to a few dealerships, the only time you would have a problem is if the camshaft cauyses a problem, then he warranty will not cover it.