…And as they came down from the mountain, Jesus charged them, saying, Tell the vision to no man, until the Son of man be risen again from the dead. And his disciples asked him, saying, Why then say the scribes that Elias must first come? And Jesus answered and said unto them, Elias truly shall first come, and restore all things. But I say unto you, That Elias is come already, and they knew him not, but have done unto him whatsoever they listed. Likewise shall also the Son of man suffer of them. Then the disciples understood that he spake unto them of John the Baptist.
It sounds to me like Jesus is telling his disciples that the spirit of Elias reincarnated in the flesh of John the Baptist.