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check out the breeder, call their vet, ask for references, have the puppy genetically tested,
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Sadly, there is no way to breed out this disease yet. The method of inheritence is not understood. There is no genetic test for CT at this time. Since Chewy has a mild form of this condition (thank god he's so large, that really helps), I have researched this issue at length.
Good for you, getting that second opinion. Dr. Tobias is EXCELLENT, he's the guy who proved the hereditary nature of liver shunt in Yorkies. He's also doing the research to develop a diagnostic test for the CT defect. In order to raise awareness for breeders and dog owners, I no longer call this Collapsed Trachea, but "Softened Trachea" since the collapse is only a symptom that may or may not emerge, while the softened trachea is the true defect to be guarded against.
I've asked several breeders about this, and they are all 100% at a loss as for preventing this. I spilled my entire range of knowlege on this subject in the Yorkie Health and Diet forum, and also the Breeders forum. Feel free to read up on some of the stuff I posted there.
I have it on authority from the kind lady in charge of the Yorkie Rescue folks and also the Yorkie club of America, that while there is no test yet, they are trying to develop one and also to learn how this disease is spread through generations. They currently believe it's polygenic (having to do with many different genes in combination), but they don't know which ones.
For those of you who are concerned...you can screen your pup with a tracheal massage. Gently massage the area around the throat both near the jaw and at the chest for about 1 minute. If it provokes coughing and honking and gagging, then you should evaluate your dog with the help of a professional. Currently, this is all breeders can do to attempt to detect the defect. Even if they could detect it, they wouldn't know what to do...Most times, a dog will pass this screening until a mild collapse event has already taken place. This generally occurs around 7 years of age. Most breeding dogs will already have several litters out there before any symptoms can be detected.