I think Barnabas went into his vampire body when he sent his consciousness back to 1897 because his body already existed at that time. As a matter of fact, keep watching the 1897 storyline - it will provide an explanation when an unexpected visitor shows up to help.
And I really like, Irishcoda, what you said if things had gone eskew and the vampire consciousness of Barnabas had occupied his mortal body in 1969. Now wouldn't that have been a hoot! Woopsadaisy! I can just picture Julia rolling her eyes, saying: "Well, that was a great idea."