The way I read it, the OP flew in J *to* HKG, and upon trying to check in for the return flight *from* HKG was informed that his co-pay payment for that upgrade was declined and he needed to pay it before being able to check in. I don't see any references to upgrading the return (and indeed his post states "upgrading from Y to J on the outbound using a miles and $350 upgrade."

If so, there was only one co-pay due and he has a CC statement showing it was paid.