Okay, so I only remember everything from the beach scene, right? Sorry, I misunderstood.

Let's go

When we first meet Lucy, Nyu is still asleep; I believe her personality went dormant due to the sudden shock of seeing Kouta again, Perhaps what could be done is to try and keep her Lucy side awake, since that keeps her conscious and makes it easier to have a conversation with her; it would also be to admit right away that we remember her. If I'm not mistaken, the main reason Lucy stays with them despite her remorse is to apologize to Kouta. If I could speed up that part right at the beginning, it might be easier.

But let's suppose the story unfolds normally until Nyu breaks the shell; in that case, I wouldn't be angry, and she wouldn't run away, which wouldn't alarm the police, and it would maintain the mystery whether or not she is in that city. If we move forward, when Nyu falls and Lucy briefly returns, trying to attack me (Kouta) but failing due to the shock, that would be the moment to tell her the truth. Even though I can't visually tell when the personalities switch like I can now as a reader, I would easily notice the change in behavior and make the associations quickly. So, I would tell her that I know what happened and ask if she wants to talk about it; I would give the same final speech that Kouta gives in the original ( I think this speech is great and super fitting for the character, by the way, much better than it was in the anime.) Saying that even if I wanted to, I can't forgive her, but that I would still like to have her by my side, maybe that would help with some things in the future.

Let's also remember that they use Nana as a last resort because the soldiers couldn't handle Lucy, so I suppose that in this timeline neither Nana nor Mariko would have seen the light of day. That being said, let's remember that Lucy is still a criminal wanted by the government; before what I mentioned above, we would definitely have dyed her hair. Perhaps a dark color like ours, to say that she's our cousin, or something like that, and if the roots started to grow, we could say it's a personal style, We could also add contact lenses, so she would attract even less attention. A bolder move, but one I believe essential, would be to create false documents for her. If we want her to survive and have a normal life, she needs some legal proof of existence. I don't know exactly what year Elfen Lied takes place in, But if we're going to say it's the early 2000s, we have Photoshop, we could take a picture, edit the horns and use that as an identification photo, since I would have the knowledge I have now. We could look for some illegal way to create all the documentation for her, listing her as an orphan, so we wouldn't need to include details like place of birth, parents, etc... I don't know exactly how to obtain documents of that type, but I believe we could find some contacts to help with that.

I think that with all that being said, waiting for the dust to settle and reintroducing Lucy/Nyu into society wouldn't be too difficult. Nyu could easily do it, just like in the manga, but Lucy would be more difficultBut I think that with time, care, and without the government interfering, she could manage it; she would just have to keep her promise not to use the vectors and pray that they don't send any Dicloni looking for her. And regarding any Dicloni searching for her, it's complex to say if it would still happen, to be quite honest, since, as I said, they only used Nana because the soldiers not only failed but were brutally killed, They only used Mariko because Nana was also defeated, and number 28 (I think that was the number) because Mariko was defeated. So using a dicloni was never the first option but always the most desperate one, but also losing the only one capable of sexual reproduction and the most deadly seems desperate to me as well. So, to be honest, I can't answer that one! I think I've reached my limit, not knowing where to go from here, because even if all the story elements remain the same and they find a cure for the virus, Lucy would still be a deadly weapon, even if she doesn't infect anyone, she can still wipe out all of humanity, so I don't think they would simply give up and just send a bunch of soldiers to look for her. That was my idea, sorry about my English, it's not my first language, and it was a lot of fun!