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Hello, I'm Dr. Deb.
I recently came online and see that your question hasn't been answered. I'm so sorry that you've had to wait for a response, but if you still need assistance, I'd like to help if I can.
This isn't actually as uncommon a problem as you might think. DNA testing can be done after the pups are born and you can even register the pups if they are AKC registered once the sire is known. All you hve to do is contact AKC since they have a procedure/process which has to be followed.You'll be sent materials to do cheek swabs on the pups, dam and two sires.
I hope this helps although, again, my apologies for the delayed reply. Deb