Old Post, but seeing as I had the same question back then, I'll just answer. It's actually quite simple, that was either the author who made a mistake, or he just felt that the second nascent soul had outlived its usefulness so he decided to make it disappear (and no it didn't die back then after the encounter with the 2 devil ancestors clones, as it is very clearly mentioned that he recovers it after it escaped in multiple fragments, and it recovers its cultivation very quickly with all his pills). It most likely is caused, by him at this point, being in a rush to finish as you can see the quality somewhat drop and the content appears lacking with some parts rushed, missed, a lot that could have been expended on, and some things that could have been explained and detailed a lot more, as such a mistake/oversight early on would have never happened. Personally I didn't mind that much since I was planning to read the Immortal World arc and I kind of felt that we needed a change of setting, but it was kind of a shame for the lack of details and expansion on some parts.
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.