The short answer is yes, duct cleaning, done right by a reputable company will help with the smell. It is likely though the smell is coming from another source, ie the crawl space. It could also be that another rodent is dead in the duct work. A visual inspection would be in order to check for any breach in the duct system. A duct pressure test would be able to tell you how much air is leaking from the system over all. A hole large enough for an animal to enter would loses a great deal of air, over 300 CFM. It would be worth looking into having this test done and it should cost around $200. Cleaning the air handler and evaporator coil will greatly improve the performance of the air conditioner. Dirt and dust on the evaporator acts as insulation and reduces the amount of cooling done be the coil. Any quality duct cleaning should include cleaning the air handler and coil, and the tech should allow you to watch him perform the work as it is done.
The key to the continued and efficient operation of your heating and cooling system is periodic maintenance. Cleaning the air duct vent system, and servicing you heating and cooling equipment will keep the system operating at its peak performance. Air ducts are cleaned for two reasons. One: to prevent debris from entering furnace and air conditioning components. Two: to prevent debris from cycling through the home. The air duct cleaning contractor needs to employ cleaning methods which successfully removes debris, and ensures that debris does not enter the occupied space. Most contractors can verify the results of the cleaning through video or pictures.
On the other hand, if a service provider fails to follow proper duct cleaning procedures, duct cleaning can cause indoor air problems. For example, an inadequate vacuum collection system can release more dust, dirt and other contaminants than if you had left the ducts alone. A careless or inadequately trained service provider can damage your ducts or heating and cooling system, possibly increasing your heating and air conditioning costs or forcing you to undertake difficult and costly repairs or replacements.

I purchased one of those Amazon air duct cleaning coupons for 49.99. When the company showed up, they removed the vent closest to the air intake and immediately told me I needed $1800.00 for all new duct work. They said they could not clean the system until new duct work was installed. I thanked them and said I would give them a call. The only call I made was to Amazon to get a refund. I know I didn’t need new duct work. Be careful to not fall for unscrupulous salesmen and their pitches and scare tactics.
As a person with severe mold allergies, I live in a the South where the climate naturally breeds molds.We noticed a difference when we had our ducts cleaned.The company used a vacumn type system and covered all of our vents with plastic that was held up by the suction. We had no damage, no leaking dust/dirt back into the house and it took several hours. I think if you use a reputable company it makes the world of difference. Now we use better air filters and also have a UV light to prevent mold growth on ours system.We 'd do it again when the time comes. From your car's air filter to your dryer...anything works more efficiently when it is not filthy dirty.That's just common sense.

Duct cleaning has never been shown to actually prevent health problems. Neither do studies conclusively demonstrate that particle (e.g., dust) levels in homes increase because of dirty air ducts. This is because much of the dirt in air ducts adheres to duct surfaces and does not necessarily enter the living space. It is important to keep in mind that dirty air ducts are only one of many possible sources of particles that are present in homes. Pollutants that enter the home both from outdoors and indoor activities such as cooking, cleaning, smoking, or just moving around can cause greater exposure to contaminants than dirty air ducts. Moreover, there is no evidence that a light amount of household dust or other particulate matter in air ducts poses any risk to your health.
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