You have to assume that both studs *could* have tied with the female, regardless to if you witnessed it or not. There should be no question as to if she and the borrowed stud tied--they should have never been left together unsupervised, for more reasons that one.
But, hindsight is 20/20, or so they say.
All of the pups will have to be DNA'd to determine which pup goes with which daddy. To make sure that their registration and your records are correct, to be able to present the new owners with the accurate information at IF the borrowed stud did sire any of the litter, to fulfil whatever end of the arrangement that was made with his owner.
Just chaulk this up as a lesson learned so that you know how to prevent this type situation in the future.