I think you would be wise to ask a doctor. Whilst I do not know what would happen to the cyst(s) I know that they can (even at ground level) cause or help to cause a DVT because of the pressure and possible restriction around the popliteal vein.
My, non-professional, advice on the tansit would definitely be to take all measures to help prevent a DVT. Seriously consider wearing support stockings and keep moving and don't get dehydrated. At the very least read up on DVT. Also try searching for Baker's Cyst and DVT, there's lots there.
If you get a DVT, not only is it potentially life threatening, but you would then be off flying for around 6 months.