Note there is a difference between "Negate" and "Cannot be Negated".
So in your scenario, James is the first attacker. He bands John into battle. John's ability activates, and from that point on, he is preventing special abilities on Evil Characters. So that means when Sapphira blocks, her special ability has no chance to activate, so she doesn't stop the band (or any enhancement abilities)
However, there is a card called The Twelve-Fingered Giant whose ability says "Negate banding. Cannot be negated". Cannot be negated means that John's ability doesn't prevent his ability (because Cannot be Negated means that it can't be stopped by a prevent or an interrupt ability). Thus, if Twelve-Fingered Giant blocked James and John, the band would be stopped and John would be kicked out of battle.