I'm finally back in Dubai! Thanks to everyone who provided adviec on this thread.

To wrap up the loose ends, there ended up being 2 boarding passes issued for 5D -- mine went through but then the original passenger in 5D was moved further down the cabin to I think a seat in row 9; the cabin crew came up to me to check my boarding pass at one point after I had sat down, but didn't explain why they were asking but I did overhear that there were 2 passengers booked for 5D. The J cabin ended up being full but no downgrades to my understanding. When I was rebooked into that seat, the agent in the lounge showed me a seat map that had 12+ empty seats. Being 8-9 hours from departure, I suspect not everyone had checked in / assigned seats yet.

My luggage, on the other hand, was a different story -- both AF staff in MAN and CDG assured me that my luggage had been loaded (in MAN as the handover was from VS to AF, and in CDG due to the IRROPs and flight change). When I got to AUH, I was informed that my luggage was still in MAN and would be taking the EK flight this morning. False assurances at from AF agents at both gates!