Brothers in Arms is a mod for The Witcher 3 that combines bug fixes with restoration of cut content. It's a frequently updated mod—last time we checked it restored a bunch of dialogue, including a Yennefer romance scene—but the most recent update is particularly substantial. The lengthy list of additions in version 3.1.0 includes the note: "Restored a completely new plotline - Shani's fate during Hearts of Stone expansion. Features a new ending for the expansion (optional)."
As shown by YouTube's exhaustive Witcher 3 documenter xLetalis in the video above, this plotline helps explain why Shani returns in the Hearts of Stone expansion. At one point in development her life would have been at stake if you crossed the expansion's villain Gaunter O'Dimm.