It seems that before they entered the "Sea of Souls", Qi He had already reached some sort of agreement with the program. Although the blue Sphere appeared still very reluctant, it eventually abided by the pact.
Lu Xiang witnessed the entire process of Qi He's figure gradually becoming blurred, then scattering into points of light and disappearing before her.
A confrontation between a person and a Sphere lasted for a moment, but in the end, it was RT6 who broke the silence.
When Lu Xiang conversed with Qi He, she was not present.
Both she and the "King" were not very knowledgeable about the Dark Age. Their mother created them after that era and assigned them completely different missions.
RT4, who had lived through that era, had always maintained silence, never mentioning the specifics of that war to them.