Hi there !
Not the same case but pretty much.
Bought my flight AF coded but EY operated.
Got all the EY Gold perks, even if my flight was coded AF...
Got miles on Air France Flying Blue but not Etihad.
Had 4 PNR, could not choose my seat either on AF or EY Website but my status was well recognized on each of them.
I was able to check in 2 luggage with the extra 15kgs, no issues.
EY Call Centre was clueless and could not help me on anything.