There were two souls and Naksu’s soul is stronger than JBY’s soul. JBY’s soul is clinging to Naksu’s soul energy (mage energy). Master Lee had to get rid of JBY’s soul to allow Naksu’s soul energy to transform the petrified body. JBY’s soul can’t transform the petrified body into a human again. That’s why her body transforms from JBY/MD/JSM to Naksu/GYJ. But the flesh and blood are still JBY/MD. Only her features transform.

e.g., Think of it like plastic surgery. Or Melting the clay and shaping it again.

For detail:

EP 2

31 Minutes

EP 3

20:15 - Jin Mu said that JBY's build and aura were completely different from Naksu's.

Naksu was neither that dainty nor small (which means that only her features change and not the whole body).

Good explanation. Also both souls (Naksu/Jin Bu Yeon [pristress]) somehow shared a body since season one. If I remember correctly, JBY even took over her body once in Master Lees/ Master Hemps hut  when Naksu/Mudeok was sleeping in season one. Both Naksu and JBY even met in a dream .

Now in season two it is still the same body only transformed after the healing attempt of Master Lee. So I guess both souls are still in there but now JBYs soul is awake and Naksus soul is inactive/healing. There are signs of that when JBY touches Naksus stuff. Even the blue souls switching markes flashed up once...

 Slim Xtra:
So I guess both souls are still in there but now JBYs soul is awake and Naksus soul is inactive/healing.

Only one soul left now and it's Naksu's soul. Naksu's soul had done healing and Naksu is active rn.


 Slim Xtra:
There are signs of that when JBY touches Naksus stuff. Even the blue souls switching markes flashed up once...

When Naksu got her memory back and divine power, JBY's soul might be back. But by ep 2 explanations, only Naksu's soul is left. We only have 10 ep so I don't think JBY's soul will be back. 

But there is a chance. Nah. It will bring them back to square one like in part 1. Two souls one body again and complicate the matter for Uk.

Let's just go with one soul, Naksu as Master Lee explained in ep 2.

It was never one soul because they both ( Naksu/ JBY) shared a body from the get go. So either Master Lee deleted one oul but I do not think so. He allready had the chance to "delete" Naksus soul in season one as he allready knew Naksu soul shifted into JBYs body then. Also now JBY with her powers or part of it like seeing energy is active and Naksus souls only wakes up after touching for example her sword. Otherwise its totaly unexplainable that one body now has both soul powers...

 Slim Xtra:
seeing energy is active and Naksus souls only wakes up after touching for example her sword.

Seeing energy is the divine power from the body.

Naksu's soul didn't wake up when touching her sword. She is awake/active all the time. She saw her memory when she touched the sword.

Ok, we will see but all powers in this fantasy world come from the soul and not the body... In season one Naksu allready used the soul power of JBY when calling the ice stone. Also if I remember correct Master Lee once explained that Naksu did not really soul shift into JBYs body but was "invited" into the body. I do not believe that one soul invited another soul by just surrendering the own body which is simmilar to siucide.

But I guess we will find out in further episodes. Untill then I have my theory and you have yours 😉.

Hmm ok editing is not working for me therefore this double post.

The invitation of Naksu into JBYs body explained why Naksu shifted into JBYs  weak body. She performed the soul shifting spell initially to take over a different body and wondered why she shifted into JBY/Mudeoks weak and blind body. She thought the spell went wrong...