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  If it has gotten worse since the vet last saw her, I would have it checked out if only for my own peace of mind.  These little dogs have delicate tracheas and they can be injured by pressure on the throat...  such as leading on a leash with a collar instead of a harness.  
 If the trachea is ruled out as the cause, you might ask your vet about allergies.  I had a non-yorkie who made that honking noise and it turned out her post-nasal drip was the cause -- whenever she would get excited she would aspirate some of the phlegm and then start "honking" to try to expel it.  Used to scare me out of my wits (what there was of them).  We got her on antihistamines and she very seldom had a phlegm problem after that.
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