This was an issue back in the beta patch as well (which im not using now) but she always appears on the beach just fine, its when she's on your ship that she'll just straight up vanish. Even across saves, as i have saves right next to her (she's even in the photo) and she's just not there when it loads. I've check all across the ship, below and aboce deck every time and shes gone. This has been an issue across multiple play throughs. I've been using imports so I'm not sure if a custom world state still has the same issue. It may also be possible that she'll just poof back up later but so far she never has (and I have been testing it out, save scrumming to the highest offense and just continuing playing as much as I want to without my character's daughter). When she is around she'll oddly use default sailor responses. Which makes me think they may be some kind of "conflict" between sailor mechanics and her. She never shows up as usable crew in the menu, and the wiki says she's suppose to be a companion (which I have found no hints of in game). In game she's only just been an NPC with no fancy bells and whistles. without a clear cut answer to what she's suppose to be I can't tell how these systems are suppose to treat her.
So if anyone else has this issue, thats are far as my technical help can get you. Save nearby her and pray.