When James and his friends ventured into the World Between the Worlds, Lucy ended up being killed by Judith, the Lady of the Lake. Lucy's parents were left shocked by her death, which was still seen almost six months later, when James noted that Percy had a empty look on his face that never fully went away. Her funeral took place some time before the events of the Morrigan Web, and left a profound effect on the rest of the family.
James blamed himself for her death, to the point that he accidentally called his sister, Lily as Lucy during a night outing. Rose also felt guilty for Lucy's death for not trying to stop James from entering the World Between the Worlds.
She was seen with Arthur Weasley when James and his father looked into the Mirror of Erised. And although she didn't say anything, he was still brought to tears at seeing her.
However, Lucy is later resurrected when James Potter and Petra Morganstern travel back in time and Petra sacrifices her life, thus creating a new destiny where the Crimson Thread was never taken and Lucy never died in the World Between Worlds, thus attending Hogwarts and being Sorted into Hufflepuff House. James encounters her soon after awakening from his fever and is overjoyed at the sight of her.
In the epilogue, James mentiones that he did see Lucy romantically for awhile, and she is currently studying for her doctorate in advanced technomancy at Alma Aleron.