JP was a victim of the witch Katja.
Background
JP was a frequent visitor of the Round-Up, and was often accused of stealing tips. One night, he was thrown out by the bartender, who swore he'd kill him if he ever saw JP again.
JP walked back to his car, apparently drunk, and was approached from behind by a mysterious man. He subsequently vanished, not to be heard of for days.
This led Sam and Dean to arrive at Pendleton, Oregon, to investigate the case. A homeless man who witnessed his disappearance claimed it was done by aliens. Tina, another regular at the bar, mentioned that JP was a harmless person.
When the same guy who took JP kidnaps a rejuvenated Dean and Tina and locks them in a cell, the two discover JP there, also rejuvenated. He and Tina share a cell while Dean is kept separate.
The man, Hansel, eventually comes back and takes a terrified JP away, managing to knock Tina aside when she tries to stop him. JP is presumably cooked and eaten by the witch.