The new Forgotten Realms books are set after Baldur’s Gate 3 and show Karlach found her happy ending, though one jerk wizard also dodged his comeuppance
The idea of “canonicity” in RPGs is an odd one, given the whole point of both videogame and tabletop RPGs is that the players decide what the main characters do. But sequels, spin-offs, and sourcebooks have a habit of choosing particular outcomes as the “real” ones—unless it’s the Elder Scrolls, where every ending of Morrowind happened at once.
Baldur’s Gate 3 had to deal with characters from Baldur’s Gate 2 having canonical events happen to them between games, like Minsc and Boo being turned to stone or Viconia and Saarevok backsliding into evil, and now the cast of Baldur’s Gate 3 are in the same boat. The latest Forgotten Realms supplements, Adventures in Faerûn and Heroes of Faerûn, move the timeline on from 1492—when BG3 happens—to 1501, and hint at the fates of its cast.
Quotes from Karlach crop up throughout Adventures in Faerûn and she appears more than once in the art for both books alongside Astarion, Shadowheart, and Minsc. And in none of those illustrations is she a mind flayer or a pile of ash—two of the potential outcomes for her in Baldur’s Gate 3.
Although if you helped Shadowheart achieve her redemption arc it’s entirely possible that in act three you told Dame Aylin about the jerk wizard Lorroakan who wants to steal her immortality, and she wrecked the dude as he so richly deserves. According to Adventures in Faerûn that didn’t happen, and Lorroakan is still alive and holed up in Ramazith’s Tower. However, it’s mentioned that he was “Humbled by a recent failed bid to achieve immortality through undisclosed means,” so at least he didn’t succeed. Presumably the canonical PCs lied to both him and Dame Aylin, preventing the conflict from ever happening.
Astarion gets his own supplement in a digital add-on called Astarion’s Book of Hungers, which includes rules for playing a half-vampire dhampir as well as a string of adventure outlines where you get to hang out with everyone’s favorite vampire spawn, although these are noted as being set before the events of the videogame. No canon conflict there.
It’s not all videogame characters in these books, of course. The heroes of the D&D cartoon make another appearance, just like they did in the movie Honor Among Thieves, looking slightly older and perhaps a bit more competent. Elminster rates a mention too, though he’s said to have been missing for a few years, which conveniently explains why he’s not around to solve whatever problem your own players are involved in.
