You can easily set it to keep the default Japanese language and English subtitles for the anime and Eglish audio and subs for everything else. I created 2 profiles. Main profile for everything non-anime to keep english audio and subs and an anime profile to keep Japanese audio and English subs. It remuxes everything, keeps it all in its directories and doesnt change filenames or anything, juat removes unwanted tracks and subs and library remains intact in Jellyfin/Plex.