I find it hard to believe that they were not allowed to complete the flight as a one off waiver or did the extended flight at FL 270 mean they didn't have enough fuel to reach Warsaw.
You do realize that primary radar coverage is more or less a thing of the past? Allowing a non transponder aircraft in would effectively level cap all the airspace it transits for all other aircraft. Very few overland ACC controllers have current procedural ratings, so the LOT aircraft would inconvenience a lot of other aircraft. (Contingency procedures for handling non transponding aircraft often involve "generous" separation minima.....)
Best let LOT get all the inconvenience......