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What if when the OP checks in with LY and the LY system is unable to see which seats tje AA has system has assigned?
I had a DL itinerary, held by DL, but the ticket had to be issued by AF, as I was using an AF issued e-cert.
AF had to generate another booking with its own PNR to issue the ticket. I was afraid that this would make me lose my seat assignments with DL. Fortunately, when AF duplicated thr DL itinerary, they did not generate a new DL PNR. Somehow DL PNR did not transfer my credit card info to AF and AF did not issue the ticket for lack of PNR info. When the ticket had not been issued for more than 24 hours, five days before the travel date, I called and was assured that it would be issued soon. This prompted AF to call me to get the credit card info. Iade sure that all my flights were DL coded. They were all on DL metal. Had they been AF coded, I would have lost the ability to change seat assigments in case a better seat opened up closure to departure, especially for the return leg on which I was eligible for upgrade.
I was able to change to a better upgrade seat. Yet communication was less than perfect. The AF PNR reflected my Diamond staus on DL, but not my Million Miller status on DL.
No harm done. I would like to knoe what happens to OP's seating at the time of check-in.