Could i fly with heterozygous factor v leiden and existing clot?

Yes, you can: Yes if you are on adequate anticoagulant therapy.

Are you on anti-: Coagulant treatment? I trust that you are being treated with a long term anti-coagulant. It would be prudent to discuss the matter with your doctor, as depending on the anti-coagulant you may need regular monitoring. A short flight is not expected to add to the risk.