It just struck me, Aabria's description of Deanna's backstory just illuminated what happened with Molly and Kingsley.
When The Mighty Nein resurrected Lucien with the hope of getting Molly back, they didn't expect someone 'new' would come back out of that mess. After Jester restores his mind, Kingsley talks about what it was like being in the Moonweaver's domain.
Molly was only ever a fragment of Lucien's whole. Something left behind in Lucien's body, just enough to let the body come back after everyone thought he was dead. A 'cutting' of a soul, left behind to regrow into a new tree. Lucien was able to will himself to stay together, to not disperse after he died. To seek a return in whatever way possible. And when Cree resurrected him when she learned of Molly's death, Lucien happily returned with no hesitation.
But when Molly died, his new soul just returned to the Moonweaver's domain, blending with the rest of the ocean of souls. When Caduceus called upon the Wildmother to 'put him back', she probably scooped up what had been Molly's soul, which had now mixed with the ocean of souls, becoming something new. That's why we got Kingsley instead.
I haven't read the 'Nine Eyes of Lucien' book yet, but I believe there's references of how Molly kinda exists in Lucien's head after Lucien returns. It's probably like an imprint of his soul & memories left in his body. That anchor that let him come back as Molly the first time.