Hi i am Dr Ahmed Aly
thanks for using healthcaremagic site ,
I had gone through your question and understand your concerns ..
Sometimes
OCD ( osteo chondral degeneration ) is missed with doctors as it show symptoms of alot of many other joint diseases that may cover its significant presence usually CT and
MRI are more diagnostic than X rays especially in such lesions which maybe tiny or small .
For the clot i thing it may exaggerate the degenerative conditions of your ankle joint due to the degeneration of the cartilagenous part of the joint . Thus allowing more bone friction without cartilage chondral surface for joint mobility and causing loss of cartilage texture even more than before .
steroid injections , endoscopic interventions and surgical removal of such
cyst may be asked by your physician after proper diagnosis .
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Any further clarifications feel free to ask.