Maybe Craig Slocum was unavailable for that episode for some reason. They didn't make an announcement on the cast change during the title sequence.
Edward Marshall, the second Harry Johnson played a young Ezra Briathwaite in 1897.
There are a few characters on DS who disappear on DS without explanation...Harry Johnson, Tony Peterson, Frank Garner, Magda, Buffie Harrington.
The most likely scenario is that Harry left Collinwood during the time Barnabas was in 1897, probably because there was nothing to do there anymore.