Renewal Approved Timely But Recorded Late

We have a small (36 home) subdivision located in Georgia with no amenities and the only common area is a small front entrance. Our covenants expired December 31, 2013. They were the original covenants from the builder, 20 years prior. We spent a year gathering opinions, forming sub groups, presenting drafts, and then a final copy of updated covenants for a vote. Vote passed with only 3 homeowners voting "no". We met the requirement for renewal and our Secretary was supposed to file them with County prior to deadline. She failed to do so and we didn't discover this until January. We filed them immediately. The 3 homeowners who voted against the covenant renewal included the Secretary. The trio was upset about personal matters. Their opinions and suggestions were all accepted and approved in the new covenants. They refused to pay dues and continue to state that because covenants were filed late, they are not legal. Everyone else has maintained that the vote and approval was by deadline. We have had homes sell using the new covenants at closing; we've had Architectural Committee requests presented, approved, and acted upon using the new covenants; and we have collected dues and filed liens with the new covenants. We now have a new HOA president - who was once a party with the trio of naysayers although he did vote yes. He is insisting that the covenants aren't valid and that they be scrapped and completed again from scratch. Per our original and current covenants, that requires 100% vote - which we know will be impossible. Doe anyone have any advice on whether the current covenants may be legal as they have been utilized in legal proceedings although filed past the deadline?