James and Lucy ultimately end up together after the events of the "Where Are They Now?" Epilogue.
"In the years to come, she told him absolutely everything." sounds like they go on to have a much closer relationship than the Epilogue seems to imply (where she is studying at Alma Aleron and they've dated on and off for years). James and Lucy will ultimately end up together after the events of both epilogues. Petra will be the new Gryffindor Ghost, but will wait until James is no longer the Headmaster of Hogwarts.
She will avoid hurting him again by not letting him know she's there until the next generation, much like Cedric did.