Pulmonary Embolism Support Group
By far the most common form of pulmonary embolism is a thromboembolism, which occurs when a blood clot, generally a venous thrombus, becomes dislodged from its site of formation and embolizes to the arterial blood supply of one of the lungs. Symptoms may include difficulty breathing, pain during breathing, and more rarely circulatory instability and death.
When your clots are gone and when you start to feel better are two totally different things.
Here's an FAQ topic from ClotConnect that addresses the question in general, for both DVTs and PEs
http://patientblog.clotconnect.org/2012/07/26/faq-when-will-my-clot-and-pain-go-away/#more-1719
So, if your clot seems to be taking forever to disappear, don't give up hope.
Hugs, Cindy
http://www.medpagetoday.com/Pulmonology/SmokingCOPD/13164