It sounds like the breeding wasn't released by the stallion own. You say the same man owned the mare and sire prior to your purchase of the mare. The breeding report was filed so that's good, but now the stallion owner needs to release it for registration.
Because he, his wife, and son are deceased, you need an affidavit of heirship filed with a release. The affidavit needs to be signed by the stallion owners heir or you need a different affidavit from the personal representative/ executor of the stallion owner's estate. AQHA will not help you track these people down, but if you provide them names and addresses in writing, they will probably help you with the paperwork.
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