I have a friend that recently came to Japan and while there renewed his jttp card. He wasnt particularly paying attention but he noticed something odd.

When he originally got approved in 2018 he received the card but they also placed a stamp in his passport with a QR code to scan at the machines. This time he got the new card but the agent specifically crossed out the qr code stamp in his passport but did not add a new one. Since he was a bit jetlagged at the time he really didn't check the passport only the card to make sure everything was correct.

Has any one else that's gone through the secondary inspection also not gotten a QR code stamp in the passport and had any existing one crossed out? If so I assume at the gates all it needs now is the facial recognition and fingerprints along with the physical card?