I record all of my Retroarch gameplay footage into a captures directory. It starts as MKV but I like to upscale(nearest neighbor) to 5x and re-encode using FFMPEG.

batch_mkv_convert.sh

#!/bin/sh

FFMPEG=/usr/bin/ffmpeg
SCALE=5
MKV_FILES=`ls /mnt/captures/**/*.mkv`

for FILE in $MKV_FILES; do
	DIRNAME=`dirname $FILE`
	OUTPUT_FILENAME=$DIRNAME/`basename -s .mkv $FILE`.mp4

	if [ -w $OUTPUT_FILENAME ];then
		echo "$OUTPUT_FILENAME exists removing..."
     	 	rm $OUTPUT_FILENAME
		echo "Removed."
	fi

	$FFMPEG -i $FILE -f mp4 -pix_fmt yuv420p -vcodec libx264 -preset fast -acodec aac -vf scale=iw*$SCALE:ih*$SCALE:force_original_aspect_ratio=decrease -sws_flags neighbor $OUTPUT_FILENAME && rm $FILE
done