What Causes Severe Cough With Lot Of Phlegm Even After Bronchoscopy?

I recently had a bronchoscopy after being diagnosed with pneumonia, for which I was prescribed antibiotics, three steroid shots, albuterol, breathing treatments, etc. Following bronchoscopy, was told there is a "normal" amount of bacteria still present in my lungs, but not to worry since I appear healthy and no issues with fever, blood pressure normal, and told cough would eventually subside, and scheduled for a follow up breathing test with X-rays in two weeks. But two weeks have past since the bronchoscopy, and I still have a severe cough that prevents me from sleeping, with lots of phlegm and constantly smelling smoke that no one else can smell for last five days.