Even if Nine knew Dyon had a planet grade pill, she still wasn't worried. The reason she went out of her way to inject Thirteen's body with volatile qi was to make such a method useless. She knew she didn't have the time to crush Thirteen's soul, so she made do with this method.
From Nine's perspective, only an individual with higher enigmatic qi purity than herself could dispel that qi. As a result, even if Dyon had such a pill, it would be useless. Thirteen would die after the pill's medicinal effects ran out.
However, what Nine didn't know was that Dyon was perfectly capable of this… Because he had a space where he acted as God!
After putting Thirteen into his inner world, Dyon directly crushed all of his remaining arrows with the exception of the two most powerful white-black ones. He knew that he had to give up much of what he had if he wanted any hope of controlling the extracted enigmatic qi.