When I clicked on the accept button (after getting confirmation from Aegean on Twitter that I would still get the miles), I didn't receive an e-mail confirmation. But I have just noticed on the boarding pass from 14th January that the e-ticket changed. The PNR stayed the same of course.
Anyhow, I will fight them for these miles, both the service centre agents and Twitter team told me that I would get the miles. I despise dishonesty.