In reply to duchessofmalfi: You can replace them but the cost will depend on the make and model- given they sound like their probably fox then I think they may start at around £150 but don't quote me on that. There is information available online about using nail polish to sort out scratches- takes quite a lot of work and you have to be patient but it can be effective.
Its not so much that you'll destroy the seals more that the forks may leak- I have a small scratch that has had no obvious effect on performance.