When you were upgraded, did you e-ticket change? If this was originally issued under KrisFlyer (618-xxxxxxxxxx), did that change to Aegean (220-xxxxxxxxxx) or change in any other way?

The reason why the upgrade isn't possible is because Aegean can probably not re-issue your ticket for an upgrade without assuming costs. However if they did do that (even though it was only temporarily) then you certainly have a case for compensation: You paid, were booked, and got ticketed. The regulation does depend on the being ticketed part though.