Lost in the catastrophe (Failure to back up my transfer pool) is the world renowned Across The Galaxy
This beast threw so many quality runners. I have many offspring but nothing beats the original. In my haste to stop the fire I overwrote the file again losing a couple more quality horses.
While surveying the damage I realised I forgot to backup the file from my last breeding foray. Five more horses roaming the countryside somewhere. 
This new transfer file can be a pain. Moral of the story - save a copy of your transfer pool in a separate folder. After you transfer in horses to your game copy the backup you made back in to the save folder. Presto! You have your horses to be used for breeding again and again.