I must have misunderstood, I thought you had said it had all happened since you brought the pup home, and that he was fine with the other Yorkie you brought home. So the timing really isn't a factor because he liked the other dog in your home.
Since he knows he is safe with you and you will protect him from the pup, then you need to look at other reasons he is not eating, hiding and acting depressed. However if you do think it is the addition of the pup, then what is it about the pup that bothers him? Energy? Pestering him too much? Getting too much of your attention? Not backing off when asked?
When you figure it out then decide how you can help. Typically when dogs are out of sorts it helps to create more structure in the environment. This requires more engagement, rules and boundaries, and play.
Dogs breathe easier when someone else is in charge.
Love Them & Lead Them,
~Elizabeth & Doug
Dog Training the Way Nature Intended