I feel like I might be having a similar issue, but this time with AA issued tickets and a JAL PNR.

Same issue with a changed flight time, AA reissued tickets, but the JAL PNR is showing duplicate segments, both the old and the new. I've received assurances that JAL's system will remove the old ticket numbers from the reservation at Some Point™️, but I'm starting to doubt.

This feels like a common issue in general with different issuing/operating carriers, most often with codeshares. You'd hope that there would be better coordination between airlines in an alliance but apparently not...