It's very strange. He was using his second nascent soul to store that green Qi from the crystalline beads found in the pieces of Foreign Devilish Metal. He kept doing it until he found a way to refine that green Qi.
The last time his second nascent soul was mentioned (that i could find) was chapter 2126 when Han Li had simply store his second nascent soul (so it was completely safe). After that is was only mentioned again chapter 2307 when it was said that his second nascent had disappeared.
My guess is that the author thought about and end for the second nascent, but forgot to actually write the chapter and we were left without knowing what happened.