Close Combatant Question (also applies to other archetypes)

If the archetype says “If you already have Close Combat, either skip it or swap the die with one of your new dice.” and you elect to skip it because you have the requisite thing does that mean you have one less die for the rest of your options? Does skipping the Close Combat still use a die?

No, if you skip it means you have all your dice from the Power Source to choose for options the Archetype.