Rei had one soul (which was probably that of Lillith) that was swapped between bodies (50 in total) when the old one "died", and her body was actually made up of 50% Yui's DNA and 50% Lillith's DNA. Sadly, when the soul with its memories were transferred into the new body some were lost.
Also, if the three Reis were compared with each other, it could be seen that Rei was becoming more and more human in personality, since if Lillith's soul was put into Rei 1, then Rei would partly remember being an Angel, and also the enemy of Man. Note the way she interacts with Dr. Akagi Naoko. (Personally I find this a little strange, because Lillith is supposed to be the Mother of Mankind). Yet Rei 3, who is the last one, finds herself so to speak...in EoE she even smiles!
Another thing, the Rei clones used within the Dummy Plug system all had no souls, they were just used as interfaces
15-Aug-2005