This never occured to me before about Barnabas' 1969 self sent to the chained coffin in 1897 (& probably frozen like in the present). I know that after this takes place, we never see the mausoleum again in 1897.
I always wondered what happened to his present time body after its diappearance, but it going into the 1897 chained coffin works. Off camera, Angelique could have managed to right the souls with the bodies & the medication she gave to Barnabas was for his physical well being after the body switiching.
Someone please create a justification for the idea that when Barnabas's real body disappears from 1969 while in the I Ching trance, that body materializes inside the coffin in 1897, and when he leaves 1897, his over-written 1897 soul pops back into the body that's now in the coffin. Or something.