The butterflies in Fatal Frame 2 have multiple significant meanings. To most people, Easterners and Westerners alike, butterflies signify transformation, rebirth, and the life cycle. In Japanese culture in particular, however, there are additional meanings. Butterflies are seen as the souls of people who are alive, and most notably of the dead. Butterflies are also seen as messengers of the dead, and guides to mystery or solutions to ordeals.
According to the game's creator, butterflies represent two halves of a whole that cannot function apart. Thus the twins are butterflies's wings. This is the reason why several twins in the game say "Didn't we promise we would always be together?" This butterflies are a metaphor for the unity of each set of twins. Alternately, butterflies represent the love of two people, especially when one of the pair has died. Often the one left behind is heartbroken and will commit suicide to be with them. This is how Itsuki and Mutsuki Tachibana's relationship played out in the end. After the ritual between the brothers failed to calm the Hellish Abyss, Itsuki took his own life, although the two did not get to be together in the end.
Other twins in the game suffered terribly from being separated. Akane killed Azami Kiryu, and the ritual was successful. But Akane's heart was broken after her sister's death. Yae left Sae, who was on her own afterward, and some endings of the game have Mio and Mayu separated or succesfully complete the ritual.
Of those who successfully complete the ritual, the marking on the neck of a strangle victim as killed by their sibling serve as a reminded of sorts that the two really are together after all. But how well the person takes this symbol is dependent on the individual.
It is rather sadistic to rip the wings off a butterfly, and so the separation of a butterfly's wings is at once both painful and pitiful.