I have done this before: installing 6 Plus’ battery in a 6S Plus. Battery life was slightly more but Apple Pay would not function properly (authenticated on the iPhone but unable to detect by the cashier’s terminal).
I had replaced my iPhone 6S Plus battery (2750 mAH) with that of 6 Plus (2915 mAH) since both have the same connectors. Battery life did slightly increase but at the expense of the non-functioning NFC/Apple Pay. I think it might have to do with the overclocking of the NFC frequencies out of the acceptable spectrum . I thought the slightly longer battery life wasn’t worth the lack of NFC so I installed the correct one for iPhone 6S Plus battery (2750 mAH) and NFC/Apple Pay is working well afterwards.