The transformation wasn't meant to fully convert one's body into an entity of nothingness. To do so meant erasing everything other than the nothingness itself and would merely destroy any semblance of what a person was.
This procedure was designed so that Nonexistence could find its own place within the physical body and soul. It aided practitioners in reaching a state where their bodies could house both Existence and Nonexistence without drawbacks.
For those whose Existence was much stronger, it would take a much longer time to come out of the waters. One's body could refuse to adapt to the Nonexistence, and they could also be restricted by whatever they saw when they entered the lakes.
There were many factors that trapped hundreds of thousands of people in the darkness, refusing to let them go.