>>2248243This is uncertain.
Maybe they were backuping the memories (that explains the experiment with Rei in clone tank room). Probably dummy plugs was Rei's memories and thought parrens.
Maybe the memories have passed to Rei 3 with the soul.
Maybe they were only the parts of memories and emotions.
Rei 3 clearly has connection to Rei 2. That scene with glasses, and EOE. But we don't know what exactly is that connection. Maybe she has 100% of her memories, maybe parts, maybe just feelings and emotions to Gendo and Shinji.