I called Aegean last week for the upgrade of two flights (FRA-SKG & ATH-FRA) which was a smooth experience.
(Non flex fare w/ 0PC luggage booked via a external travel agent to aegean business using the Gold Coupons...)
However they called today to inform my about the change in taxes: 1,15 Euro have to be paid extra.

Checkmytrip already shows the flights being booked in business and the other flight segments now show 1PC of luggage and "Economy" instead of "Economy Restricted".