huh?? im sorry but this is such bad writing, they haven't explained how and why it's happening at all :(
Jin Bu Yeon's body had already petrified. Meaning, everything was already a stone. Master Lee already said that the body no longer has water in it. But because of Naksu's powerful soul, the body was still miraculously alive even after being petrified. Jin Bu Yeon was clinging on that to also stay alive inside. With Jin Ho Gyeong's decision to save the body, Master Lee had to discard (or to put Jin Bu Yeon's soul at sleep inside) for Naksu's soul to take over due to its power to revive the petrified body. Because of the power of Naksu's soul, the body completely healed. And because it was her energy that was used to heal the body, the features (face) start to resemble that of Naksu. The body and the soul must become one. That's the reason why the face became that of Naksu. This was needed because her body already petrified. But once Jin Bu Yeon completely gets her divine powers back and Naksu gets her memories (clash between the soul and the body), then either the body will petrify again or one of them will perish.
I hope this time you already get it. It wasn't really bad writing. If Jin Bu Yeon still has her original face, then the whole season 2 would just become full chaos (due to what she had done 3 years ago prior to season 2).
I hope this time you already get it. It wasn't really bad writing. If Jin Bu Yeon still has her original face, then the whole season 2 would just become full chaos (due to what she had done 3 years ago prior to season 2).