[She knows it is true. Her third self still betrayed Ikari Gendo for Ikari Shinji, even though she did not have all the memories of the connection formed while she was in her second body. If their connection was strong, it would transcend something as simple as memory loss.
But how can she explain that? It will take far too long to explain her multiple bodies, the nature of her soul, her unusual bond with Ikari-kun.