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If I use JMB miles to upgrade a ticket from PY to J, am I still able to credit the flight to another program (e.g. AA) or will it force me to use my JMB #?

Thanks

You can of course credit the original flight (in PY) to any other JAL partner.
You may likely need to retro-credit, and so keep your boarding passes until the miles post.

Once the upgrade clears, simply go to manage my booking and switch it to your preferred FF account. In my case, C-F I could not choose 2A with my JMB number in my record as it is reserved for elites (i'm a base member with JMB), once I put in my AA number (I'm CK) I was able to choose any open seat Same was true with my connecting flight where only C was offered.