To my knowledge, Apple Pay works solely through the NFC antenna, so that is what I would suspect is causing this issue. Perhaps during the repair the antenna was only slightly damaged, allowing for wireless charging to still work but breaking the NFC capabilities? That would be my only guess. If you want to replace it its reasonable cheap online.
Otherwise I do know that Apple stores card data in the Secure Element on the phone, and if that is causing the issue that’s a microsolder repair which is way beyond my expertise, but personally I would take a shot at replacing the antenna.
Good luck!
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