I'd be upset and torn about it too. IMO, refunding the fee rewards the person for not doing the right thing for the horse. Just thinking out loud here, but "goodwill" for who? You extended goodwill by everything you did. Again, jmo.
"When a president can pick and choose which laws to follow and which to ignore, he is no longer a president. " Ted Cruz
Honestly, I understand your concern for the horse but don't think you owe the new owner anything. You made repeated full disclosure and the issues seem to stem from the professional the new owner hired, not anything you did or from the horse's past. That said, I know you want a soft landing for the horse so that's the rub, obviously. If the prob is just what you and your pros think, it should resolve with a few weeks time and new owner can quit panicking. Maybe you can find a way to keep tabs on the horse and intervene later if necessary. I know that carries some risk that the horse may fall through the cracks, and keeps the situation muddied, too, but still I don't see at all why you should feel you have to give a refund or take horsie back. Maybe the new owner can be encouraged by all involved to give it 30 days and reassess.