Update - I just received an email from them. It''s not good news for now
Thank you for reaching out to us.
Regarding your request about your retro claim for your flight VL 1652 (operated by Lufthansa City Airlines), according to the information we have received from our Loyalty Department, although Lufthansa City Airlines has recently joined the Star Alliance, a bilateral agreement for the accrual of miles between AEGEAN and Lufthansa City Airlines has not yet been finalized.
Therefore, at this stage, it is not possible to credit miles for flights operated by this airline to your Miles+Bonus account.
Once the agreement is officially in place, and if the relevant terms and conditions allow retroactive mileage crediting, you will then be able to submit a new claim to verify your eligibility for earning miles from this specific flight.
Please rest assured that we remain at your disposal for any further information or assistance you may need.
Yours sincerely,