Within months of buying my house there was a smell that was almost deathly. Long, long, story short, there were a few issues. Critters made their way in the crawlspace and made a home. The ducts at some point were replaced but not all ducts were replaced. They used below code ducts and hooked them into existing ducts. The ducts were secured to a gas line and water pipes using consumer-grade zip ties (not code). They were routed like a maze and just wouldn't provide the airflow one would want. The fact that a large circle (duct) was being put into a small circle (duct) there were gaps. Gaps were filled by squeezing the ends together with more zip ties daisy chained together.
In short, I had major issues. Flex duct is not something they wanted to clean. Whether they can is another story because I am not sure. I ended up having them replace all ducts because we didn't know where the stench was coming from and I have asthma. Because of the asthma, allowing anyone to spray anything with the intention of having it "clean out through the AC" sounds absolutely wrong.
The best subscription I have ever paid for is to Angie's List. I cannot recommend it more to anyone. At the very least, it helps me make slightly more informed decisions.