"Self-flagellating" means beating himself with a flail/short multi-tailed whip. There is a scene in the original where Judge Turpin sings of his lust for Johanna and beats himself penitantly. The theory is that it beats the impure and unholy thoughts from you, leaving you chastized and cleansed. In this case, I think he just enjoys it. This scene is not included in the video versions.