>>2248222>>2248243Rei 3 is Rei 2 that has had her memories removed, and then received a copy of old memories without the newest additions.
These additions might be her emotional and practical progress as a person. Not everything is lost however, because like Rei explains, "her heart and soul is shaped by the time she has spent existing and also socializing with others", and so while Rei might not remember or know, her soul and heart remains the same.
This is why she cries in her room alone, but she has no idea why she's crying, the only thing she KNOWS at a level much more deeper than even instinct, is that she has cried before, and that this is not the first time.
He real first time was when she shed tears as she fought Armisael.