I just had a line appear in dialog that referenced the male origin even though the perk had already been removed for quite a while. Made me think there's still some variable somewhere that indicates you once had this perk so that even if it no longer applies the stat modifiers, it can still be referenced in text? The line was actually not dialog per se but more a narrative comment (MC's thoughts?), something referencing having been in an accident and now "without a penis" I believe.