Several of my collegues have had thrombosis after long days in a cockpit seat. One of them almost ended up amputating some of his leg due to this an another one had the clot trapped in his lungs and fortunately not in his brain.
As long as you are seated the clot very often stays in your feet but upon starting walking around it can follow the bloodstream to some more dangerous place in your body.
So my advise is to leave the seat at least once an hour just for a short walk or stretch.