Windows: download xdelta3-3.1.0-i686.exe.zip from https://github.com/jmacd/xdelta-gpl/releases/tag/v3.1.0
Extract the EXE file to this folder and name it xdelta3.

Linux: you know how to install xdelta3 ;^)

To get the patched episode, copy "[Strelizia] Musashi Gundoh - 13 [DVDRip x264 AAC] [2DC6BED4].mkv" to this directory.

Now run
xdelta3 -d -s "[Strelizia] Musashi Gundoh - 13 [DVDRip x264 AAC] [2DC6BED4].mkv" "musashi_13v2.xdelta" "[Strelizia] Musashi Gundoh - 13v2 [DVDRip x264 AAC] [E4D05600].mkv"

If you're on Windows you can just run patch_windows.cmd to run the command for you.
The batch torrent will have the fixed episode.