On the regsitration form there a couple of boxes you tick,the registered owner of the dog i.e the breeder can apply to have any of the following placed on the records of the dog,progency not eligble for registration and not eligible for the issue of an export pedigree,the codes need to be included next to the puppy if the breeder wishes to place endorsements.

The OP has said the bitch has endorsements on her KC certificate therefore,if any pups are produced they can't be registered.She should have asked the breeder to lift the endorsement and the stud owner the OP,should have made sure the bitch was not endorsed before agreeing to the mating.