Hi there, my baby bella had the same thing not too long ago, and I got so mad because the vet was never clear about her condition, told me to give her the medicine, then she got worse I had to take her to the Aminal Clinic at 2 in the morning...... I didn't know what to do. So went to the vet one more time and they did x rays on her but still couldn't see anything wrong with her.... They said it could be kennel cough or something that yorkies have as a genetic thing, wich is when their breathing pipe closes for a couple of seconds and the cough....... The vet recommended to give her the cough medicine once daily if she starts to cough, specially nightime, then I asked her for how long? No answer.........
So I went and checked a lot of websites that have natural remedies for dogs and I found a lots of things that you can try and it wont harm your dog..... If you're up for it.... I went to the natural food or vitamin store and got DROSERA...... they sale in little tiny balls and you give it to your dog 3 times a day or less if the cough is not that severe...... I can tell you bella's cough has been reduced to 10% of what she used to be...... I hope it helps your baby too...... If you have any questions don't hesitate to ask.....
Good luck!