This is the sort of thing that needs to be worked out in the stud contract signed at the time of the breeding.
Usually they indicate "live pups" which it sounds like she had. Still, it might be a kindness (if the other pups don't make it) to waive the stud fee.
And I would check your boy. There are sexually transmitted diseases that cause sterility in males and kill off litters of pups in utero or shortly after birth. If she already had something she might have transmitted it to your boy; likewise, if he has been used at stud he may have given it to HER.
I assume you had at least a brucellosis done, but at any rate I would ask the bitch owner to identify the cause of the infection so that you can check your boy. If they don't know, they can find out by doing necropsies on the dead puppies (which is what should be done when the first and second die, so as to save the others if the problem is treatable). If they already know what it is, you're ahead.