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.
I think I'd do a couple of things on this. First, do some of your own research. You might check Clot Connect (where I found a link to the following article: http://vmj.sagepub.com/content/20/2/193.full.pdf+html). Also, www.stoptheclot.org is another good resource. Both sites might be able to give you some research and statistics related to prothrombin.
Also, you need to ask yourself what you personally would feel comfortable with. It can be hard to know in the heat of the moment, but give yourself some time to really think through what you *feel* about the options. It's really up to you to decide what is best for you and your family and your future.
From my (admittedly brief) review of your situation, it does seem like you might be OK to come off. Even with the gene mutation, you had a clear cause for the clotting, since you were post-partum and that is an extremely high-risk time for clotting. You might particularly look into whether prothrombin is a bigger problem in relation to pregnancy and birth (some clotting disorders are more affected by this than others) or whether there are situations where prothrombin can be more of an issue.
Definitely go to your next appointment armed with questions. Take another person with you if possible (I tend to take my husband when I've got a doctor's appointment of real importance, like discussing surgery) because he/she might be able to think of questions that you haven't thought of.
Ultimately it is up to you. Doctors can give different advice, but you have to be comfortable with what you do or don't do down the road.
I've been reading some research articles online and discovered a few that say that people with Prothrombin Gene Mutation are no more likely to have an increased risk of having another DVT or PE than someone without so that is positive. I didn't realise that some clotting disorders are more of a problem in pregnancy so I must look into that. I had no complications with my first baby but I was on heparin for most of that pregnancy unlike my 2nd pregnancy. The haematologist sent off my blood to be checked for antiphospholipid antibodies. He was pretty shocked I hadn't already been checked for this, it was the first time I'd ever heard of it myself.
Thanks again :)