Had the often need to convert MKV to MP4, found this pretty cool method taking advantage of WSL and FFMPEG.

Pretty simply:

bash.exe -c 'for i in *mkv; do ffmpeg -i $i -vcodec copy -acodec copy $i.mp4; done'

And then you create a windows shortcut in the current directory, like this:

And change the "Start In" field to reflect your target directory.

You could install FFMPEG natively on windows to achieve the same end if you wanted.