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Technically, history has still not been changed regarding Barnabas being in the coffin, since only his consciousness has been sent back, occupying his body which existed back then. His physical body is still in 1969. Of course, as the story progresses, his physical body is also shot back into time, "melding" with his body back then. Most likely, if that would not have happened, once he resolved the situation (which creates another paradox anyway, but we won't go into that now), I would surmise that his consciousness would return to his 1969 physical body, while his body back then would find itself once more back in the coffin. Now don't ask me exactly how.
Gerard