I see.
Still not sure why timeline changes and/or losing Big Sister would need to get involved. I mean, yes, she's obviously a remnant from an alternate timeline from a different character-building decision, but from my (limited) understanding of timelines, if they can interact they are non-exclusive. If we can have a world which kind of has Nanami, which influences things which couldn't have existed in her source timeline (e.g, the AI on Silas's phone), we should be able to have a world which completely has Nanami.
Of course, it might act differently in this world, but there's no reason to assume it would without evidence. We don't have that evidence. Maybe Nanami is a ghost from a lost timeline, and getting anything from that timeline to truly exist would require losing everything unique to this timeline (which could make a decent conclusion for Silas's character arc, depending on how his relationship with Big Sis goes); however, she could also be "trapped" almost but not quite in our timeline, and just require the right 4th-dimensional push/pull to get her here fully.
We have no data that suggests we would lose anything by saving Nanami, and so I see no reason to assume we would. When that situation changes—when we understand what saving Nanami could cost—then we can have a meaningful discussion about if it's worth it.
...Wait, should we be having this conversation in transparent text?