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iPhone 6s Apple Pay fails to work consistently after mild contact with water during rain. iPhone housing has been replaced with aftermarket housing 3 months ago, but Wifi Bluetooth all works. Apple Pay worked reliably until contact with water. So, is it a problem with the housing, pin connectors, cables or logic board itself? Is it possible that the NFC IC is broken? All other features of the iPhone works. What is the best step to do now? Replace the housing, ribbon or NFC IC?

With water damage, you have to decontaminate the logic board before doing anything else, otherwise there will be latent issues down the road. I suspect that the NFC IC was affected by the water/corrosion. The only way to know for certain is to open the device and inspect the logic board, looking of signs of water damage. If you see any (especially underneath the logic board - must remove the upper black shield), then the logic board must be properly decontaminated. You can try to use >90% IPA and a soft brush. If that doesn’t work, then a micro-soldering repair will be necessary.