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Sacred Weapon (Su): The base damage of a Molthuni arsenal chaplain’s sacred weapon does not increase above 1d6. This alters sacred weapon.
This alters Sacred Weapon, and doesn't perform any particular modifications to it. So, you apply the modification to the Sacred Weapon ability.
Sacred Weapon (Su): At 1st level, weapons wielded by a warpriest are charged with the power of his faith. In addition to the favored weapon of his deity, the warpriest can designate a weapon as a sacred weapon by selecting that weapon with the Weapon Focus feat; if he has multiple Weapon Focus feats, this ability applies to all of them. Whenever the warpriest hits with his sacred weapon, the weapon damage is based on his level and not the weapon type, but does not increase above 1d6. The damage for Medium warpriests is listed on Table 1–14; see the table below for Small and Large warpriests. The warpriest can decide to use the weapon’s base damage instead of the sacred weapon damage—this must be declared before the attack roll is made. (If the weapon’s base damage exceeds the sacred weapon damage, its damage is unchanged.) This increase in damage does not affect any other aspect of the weapon, and doesn’t apply to alchemical items, bombs, or other weapons that only deal energy damage.
You do not change the base damage of weapons who innately exceed 1d6 damage. Your greataxe remains 1d12.