Just to report back,
As my flight were booked under AF flight number, miles and XP credits were credited on Flying Blue.
Still had my EY FF on my boarding pass, had fast track, a better seat in the plane, lounge access at MEL and AUH, cabin manager targeted me as I was EY gold, got my lunch amongst the first people served, priority line for security at AUH and luggage tagged first class.

Merry Christmas everyone.