From the moment Harun excavated the Obsidian Soul Stones, Jiyan locked her mind on one thing only: to resist all foes for 10 minutes. Regardless of the changes going on at her back, she didn't shift focus, and so didn't witness the various stages of Harun's transformation. However, the sweet fragrance and kaleidoscopic flames flickering in her beloved's eyes gave her the misconception that Harun performed alchemy on himself. It was as if his body had turned into a furnace, his heart into a flame, and his soul became the pill produced by this esoteric refinement—she was correct.
When Harun realized that his situation was utterly hopeless, that without extreme measures, all paths ended in death, he made the only choice madmen such as him would: to discard his soul. My soul isn't resilient enough? Fine, I will destroy it and create a new one. Harun's primary target was his soul, all fleshly gains were secondary.