I had the same issue, so I called up Etihad's main reservation number in the US, got connected to an agent immediately who asked for the PNR (booking reference number) and saw indeed that i had flown the flight. Said she had sent a follow-up to it and would take 7-10 days for it to post to my account. On 7th day got an email that missing miles had been posted and it also showed up on my online account.