According to the rules of this world, changing your job does not revoke any skills associated with that job, only the stats you've leveled up. The example given in the novel is that a mage that levels up and learns fire magic and then changes to a swordsman loses the stats they leveled up as a mage but can still use the magic skills they learned.
Basically this is a huge plot hole, changing her job from Temptress should not remove the skill that emits the pheromones, she should still be emitting them regardless of being a Commoner now.
EDIT: Never mind, I forgot that the fragrance skill was a set skill that only worked with that job.