Opportune Parry and Riposte (Ex) : At 1st level, when an opponent makes a melee attack against the swashbuckler, she can spend 1 panache point and expend a use of an attack of opportunity to attempt to parry that attack. The swashbuckler makes an attack roll as if she were making an attack of opportunity...
(ênfase minha)
An incorporeal creature has no physical body. It can be harmed only by other incorporeal creatures, magic weapons or creatures that strike as magic weapons, and spells, spell-like abilities, or supernatural abilities. It is immune to all nonmagical attack forms. Even when hit by spells or magic weapons, it takes only half damage from a corporeal source (except for channel energy). ... Corporeal spells and effects that do not cause damage only have a 50% chance of affecting an incorporeal creature.
(ênfase minha)
Então, Parrying é um ataque (baseado no fato de que requer uma jogada de ataque), e a criatura incorpórea é imune a ataques não-mágicos. Portanto, RAW parece ser que uma arma não mágica não conseguiu impedir um ataque incorpóreo.
Um Parry, no entanto, não causa dano à criatura, então uma arma mágica parece ter 50% de chance de aparar.