Poor Niles. I know how scary it is to have to take your puppy to the emergency hospital! I'm so sorry that you had to go through all of that, but relieved to hear that he'll be ok.
I don't think dogs necessarily react to other dogs in the same way that they do to people. If Baron is good with people in general, I don't think he'd be any different with you, if you're not any different with him. That being said, I'm no expert...so I could be totally wrong.
I hope Niles get his confidence back soon!