Hi,
I tried to claim points for several Etihad operated flights purchased through Lufthansa (because of Lufthansa connecting flights) and I was told by Etihad support agent that they flights were "marketed by Lufthansa and operated by Etihad, therefore ineligible for miles accrual."
Not sure when this policy went into effect, but it means that I can never get points with Etihad when flying the routes I need. (Since Etihad doesn't recognize said routes.)

Never had this happen with any other airlines than Etihad, and it doesn't seem that Emirates has the same issue.