I would call APHA and explain that you have gotten the horse and have a signed transfer from the breeder and explain that it's out of date and ask them how to proceed. They're going to want to know where you got her from and I'd be honest about it. They may want you to have the person you bought her from sign a transfer form and then you can put her in their name, then in yours. Most of the time they'll do it all at once. Looks like APHA doesn't have any 'penalty' fees for transferring late, so it might only cost you for 2 transfers.