SPOILERS (as if the title wasn't already one)
After Jeff Clark/Peter Bradford returns to the past, Prof Stokes hypothesizes that Peter Bradford had actually been possessing the body of a living person, and now that Peter has returned where he came from, the body was released from the possession (I believe this discussion takes place somewhere in DVD collection 12). Not too long after that, Ned Stuart arrives in town ... Since his past was never really discussed, this is plausible. It's not like Sabrina would have wondered where he went!!
This would also explain why they are identical (although in DS universe this seems like a common occurrence
)