I'm sorry this happened to you, it will be the most frustrating, stressful thing that will ever happen to you in breeding!
This happened to me on a female I bought. 1st of all, the letter AKC sends out sounds like you made the mistake, not the breeder that you purchased from. After you get through those phone calls from angry families you have sold to, and explained to all, you then begin to try to work on getting the problem fixed.
You are helpless. AKC will suspend the Breeder until she gets the DNA done on her females. The breeder does not have to comply, and can just start registering her litters with another registration.. APRI, UKC, etc.. and tell everyone that AKC is too expensive so she switched registrations....
It took me a year to get it straightened out. Thankfully, it was my female's first litter, so I only had 1 litter that was excluded until their Mom was cleared with AKC. The breeder took her time getting things straightened out, but to her credit she did finally fix it, (after a few emails of threatening to contact my Attorney). This also screws up litters of the actual mom and the other pups in your male's litter, offspring etc. What a mess!
Going back 5 years is going to be tough, and she may not still own the "actual" Mom any longer.
I'm not sure this is done on purpose, but a testament to breeders to remember that puppies from different litters should never be placed together until microchipped! Surrogate moms with their own litter is risky too.
I really hope things work out for you, and your breeder follows through!