WiseJD, I don't believe it to be that simple, so please elaborate...
All cards are AUTOMATICALLY removed from Apple Pay when performing a factory reset. I know this to be true because shortly after performing the reset on my phone I received an email from American Express informing me that my card had indeed been removed. I also called Chase to see if this was an issue on their end, and they too confirmed that my three cards with them were no longer coupled to Apple Pay.
During my technical support session with Apple, the representative agreed that a factory reset, even if restoring after the fact from an iCloud backup or an iTunes backup, will require that certain features be reconfigured...i.e. Bluetooth pairing, thumbprint, WiFi (in some cases), and most definitely Apple Pay. They remove the cards automatically upon a factory reset due to security reasons. For instance, what if I lost my phone or it was stolen? The "finder" would then still have access to all of my Apple Pay cards. Granted, they would still need to provide the thumbprint for confirmation, but are you willing to take that chance? Do you think Apple is?
I'm not sure we are talking about the same scenario, but if I'm wrong, please elaborate on your specific process in adding your cards back after a factory reset. We all just want this feature back...that's all.