It’s true that small breed dog often have tracheal problems that can cause coughing but there are many other causes of cough. First would be to determine if your pet is truly coughing. Reverse sneezing and gagging can be mistaken for cough. Recording the “episode” on your cell phone can be very helpful to your veterinarian.
Food changes can cause allergic symptoms in some pets. Coughing would be a less frequently seen sign than itchy skin or gastrointestinal upset in cases of food allergies.
Be careful making to many changes in the environment, food or medications because it may make it more difficult to determine what’s helping (or worsening) the problem.
It’s great that your pet if feeling well but at be on the lookout for signs that your pet is not feeling himself such as changes in appetite, lethargy, increased coughing especially if you see any nasal discharge or productive cough. Smaller pets often can become ill very quickly so don’t hesitate to readdress this issue with your vet and consider diagnostics such as bloodwork or chest x-rays to definitively determine the cause of your pet’s problem.