I am sorry your baby has been through so much. It does not sound like collapsed trachea if she has not been coughing or honking. What are her symptoms? Kennel cough does take a lot of time to recover from. Often, when they are on lots of medications they can develop other problems also from the side effects of all the medication.
You might want to do a little research on perhaps some natural remedy that may help her. Here is one link with some good information. Without seeing her and knowing exactly what her problem is it is hard to advise. You might consider a different vet too if your current one is not able to properly diagnose her. Some vets just guess about the proper treatment needed and they are often wrong. Please keep us posted on how she is doing.
Natural Treatments for Kennel Cough