Converts given mkv files with embedded subtitle _streams_ into _harsub_ mp4 files using ffmpeg. Uses hardlinking to overcome problem with spaces in filename of the source subtitle file.

mkv2mp4_hsubs.sh

#!/bin/bash
set -u
set -e
shopt -s nullglob

for MKV in "$@"; do
    out="$(basename "$MKV" .mkv).mp4"
    echo "CONVERTING '$MKV''"
    cp -l "$MKV" input.mkv
    ffmpeg -i input.mkv -c:a copy -c:v libx264 -preset veryslow -crf 23 -vf subtitles=input.mkv "$out"
    rm -f input.mkv
    echo "==> $out"
    echo ""
done