I'm am very sorry for your loss.
Yorkies are very prone to liver shunt, and that may have been the problem. However, this breed can be extremely sensitive to the lepto vaccine. Even if it was a shunt, the lepto could've made things worse. That isn't to say that this vaccine should never be given, but the benefit usually doesn't outweigh the risk. Unfortunately, if a shunt was present, it was genetic, so any replacement pup from these parents could also have the problem.