Yawgmoth's "subjective time" was in disarray. Humans perceive time through the cyclical firing of specific neurons, but once this function is replaced by machinery, a person's sense of time becomes inextricably linked to the machine.
This is not to say that if a human's perception of time is accelerated, their thinking can accelerate as well. In fact, human cognitive capabilities are always limited by the speed of biological electrical signal transmission. Even if a human's time sense is accelerated a hundredfold by the power of machines, they can only feel that time is passing slowly, yet their own thoughts are just as slow.
Yawgmoth had no idea how long he had been trapped in darkness. He only knew that at some point, an "obstruction" had disappeared. Thus, the dormant neurons were reactivated, and another set of memories was awakened.
