@Maverynthia Only GUI tool that I know of is Handbrake, but it's a pain in the behind to configure imho.

You could also use some simple commandline stuff:
> ffprobe -hide_banner ☆.mkv
[ ☆ is the video file; look through the list for the audio tracks and note the number of the one you want to keep (e.g. 0:1) ]
> ffmpeg -hide_banner -y -i ☆.mkv -vn -sn -map "♪" -c ac3 ♬.ac3
[ ☆ is the video file, ♪ is the audio track number you found before, ♬ is a temporary file for the lossy audio ]
> mkvmerge --disable-track-statistics-tags -o 🌟.mkv -A ☆.mkv --language 0:jpn ♬.ac3
[ 🌟 is the new video file, ☆ is the old video file, ♬ is the temporary audio file ]
And done.