Clifford79 - my understanding is that since this is an etihad flight, Virgin Australia miles can be earned. VA and Etihad are almost the same since Etihad owns a big part of VA. No chance at star alliance miles if any sort since this is Etihad flight.
I followed phoenixtinct's advice, called Aegan, was given an EY record locator, which I put into EY's system.
It let me put the VA FF number in.
Bizarrely, it seems to be showing a business class ticket, despite the original booking being in Economy. The Aegean fare class was W, which translates to EY Business class.
I wonder what the odds of them honoring a business class ticket are... they seem low to me.