"Fading puppy syndrome" is a very broad term; a lot of the time though, FPS is herpes. There are vaccinations you can get to protect the bitch; you get the first around two weeks before mating, and the second around two weeks before whelping. A lot of bitches do have the herpes virus as a matter of course, they can pick it up anywhere, and they are particularly at risk if they are pets, rather than kennel dogs, as they will be exposed to so much more in the environment. The virus does nothing to the bitch, it is only when she is in whelp that it can cause a problem. Usually herpes puppies are fine when they are born, but deteriorate rapidly and die within 3 days
It could be that the pups that died had herpes, and the survivors have a different infection
or it might not be herpes. It's impossible to say whether or not the puppies will have any long lasting medical problems. Some pups have very difficult starts and it all clears up by the time they're ready to go to new homes and you'd never notice a difference between the others ... some can be a bit "poor".
