Remove audio tracks from multiple MKV files
I don't know Windows, but I have just gone through this in Mac OS X (Linux Applicable).

mkvtoolnix is your friend here, and is available for Windows.

I used the GUI to check (a sample of) my files to make sure the audio tracks that I wanted to keep and delete were in the same order in the files. Then I manipulated the options in the GUI to match what I wanted.

Finally, I used the "copy to clipboard" button to copy the command line output to the clipboard and massaged it into a bash script to run on a directory of the files I wanted strip the audio from. 

I know it's quick and dirty (and maybe not to your liking), but you can probably use it as a starting point to massage into what you really want to do.

#!/bin/bash

for file in *.mkv; do mkvmerge -o "$file-noeng.mkv"  --language "1:jpn" --track-name "1:AVC-HD" --default-track "1:yes" --forced-track "1:no" --display-dimensions "1:1920x1080" --language "3:jpn" --track-name "3:AAC" --default-track "3:no" --forced-track "3:no" --language "4:eng" --track-name "4:ASS" --default-track "4:no" --forced-track "4:no" -a "3" -d "1" -s "4" --attachments "1" -T "--no-global-tags" "$file" --track-order "0:1,0:3,0:4";

done