Can you be a bit more specific? What instructions did you give the agent on how to enter two different FF numbers in different fields?
Sorry - just saw it now.
I asked the manager on duty if she has some knowledge of Amadeus check-in and using the FQTS and FQTV commands.
She knew instantly how to make it happen in their systems (she was a VN senior employee at Da Nang).
That's from the SQ newsletter for a flight cxl - but it is the same process.
I asked her to add my ITA frequent flyer number (starting by AZ) to use the lounge and get a priority tag for my luggage using the comment FQTS.
I then asked her to add my Flying Blue number to get the corresponding miles using the comment FQTV.
My boarding passes were then displaying my Elite Plus entitlements thanks to the status match via ITA.
I then confirmed that my AF number was correctly entered and she took a photo with her phone to show me. It was all correct.
I was able to use all my Elite Plus benefits and all my miles were credited to Flying Blue within 12 hours.
She was super quick and asked me if I worked in Aviation to know those commands - haha.
I think it will depend on how knowledgeable your check-in agent is.
From Brisbane - the check-in crew and manager on duty refused to enter two frequent flyers numbers so your mileage may vary!