You have to get all the way to the scene before the second princess (I forget what her name is) and you'll encounter the soul again at the bridge/gate or whatever before her castle. I just set the variables for both paths to be active, and I think I changed some label jumps as well to get everything in one playthrough. But yea if you convert her to dark you should get it at that point in the course of normal play.
But the main reason I wanted to post is my current theory is still that he's redoing scenes with the main characters since the sprite-overlay stuff was dogshit IMO, and I'm assuming I'm not the only one who felt that way. Having an animation on a slide show background is such a copout of doing decent scene-setting and ruins immersion. Also maybe he's writing out the cringe Shonen anime style dialogue. If there's any other reason for such an insane delay I can't fathom anything that could be good faith besides his hard drives exploding again.