A number of years before 2016, Harvey encountered a house in Tennessee seemingly haunted by a poltergeist and called upon his friend and fellow hunter Bobby Singer for help. However, Harvey was really facing a Soul Eater and his soul was taken into The Nest by it, leaving his body to wither away. Bobby eventually found Harvey when he arrived days later, still alive but dying. The Soul Eater attacked Bobby who managed to trap it despite not knowing what he was facing. The trap sealed the Soul Eater in The Nest with its victims and Harvey's body eventually withered away and died.
In 2016, the Winchesters faced the Soul Eater Bobby and Rufus had trapped and managed to kill it and free the victims trapped in its Nest. They then decided to kill the Soul Eater Bobby had faced in Tennessee. Given the decaying effect of the Soul Eater, Harvey's soul was probably not able to return to his body and instead moved on to his afterlife like The Sad People did. Harvey's body presumably died soon after Bobby trapped the Soul Eater.