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Another reason for Vi to pull out might be the phrase "Everything might have been different" as she doesn't know how to approach Jinx's "what if", because it not only implies that Vander wouldn't have "died". It also implies that Jinx, like seemingly happened in the other universe, she could have had both Vander and Silco.
Jinx being the sister that becomes the symbol is important because she is both Vander's and Silco's daughter, she is the legacy shaped by Vander's heart and Silco's ambition, even if she lacks both of them for several parts in the series. But only Vander is Vi's father, and Silco is just the main reason her life became miserable, even without being "responsible for making/forcing Jinx from Powder", so she can't step in.
Even in the other universe she doesn't get Silco as a father, or as a positive part of her life. That idea is so "other" to her that even in another Universe Vi doesn't get to experience that "what if", so she pulls away.
Damn, this scene right here where Vi reaches out to her to comfort Jinx just KILLS me every time.
It's a very small scene, but it carries so much weight because it shows how, despite all that's happened, Vi's love for her sister is still very much present, and the bitterness and resentment she felt toward her all those years ago are withering away.
I also love that when she retracts her hand, she doesn't do it forcefully or speedily, which would indicate hostility or resentment. She does it gently as if she's saying to herself, "Maybe I'll just give her some space for now."
As great as the big emotional scenes are (e.g., Vander reuniting with her daughters), you CANNOT undervalue the little moments that made them all the more impactful.