For some reason, some vets don't realize that Great Pyrenees are SUPPOSED to have double dewclaws. My vet for example removed Mokey's while she was under anesthesia for her spay. I didn't ask him to do it, he really thought he was doing me a favor. I was mortified when I found out what happened. But life goes on. I think he thought they would get caught on stuff and cause her problems or injury.
Maybe when your pup's litter was born the vet removed their dewclaws when they were a few days old...? A lot of breeders (of other purebred dogs) bring their pups in at a few days old and the vets remove dewclaws at this time, they don't even need stitches.
I hope you get to the bottom of it, and I think it's definitely time to call the breeder.