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Her being a Chihuahua mix, trachea issues could also be a cause for hacking. Trachea collapse is unfortunately quite common in the breed. My family has had many Chihuahuas throughout the years and majority of them had hacking problems and were diagnosed with trachea problems. Even a mild case can cause some serious hacking.

Since you took her to the vet I would assume they ruled out this issue, but heart problems (also common with Chis) can also cause occasional hacking. Especially with CHF as it causes the heart to swell and put pressure on the lungs. Just a couple things you might want to rule out.
 
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