On Ubuntu / Mint or any other debian platforms we can easily convert mkv video files to mp4 files using the libav-tool .
avconv is the replacement for ffmpeg.
user@computer:$ sudo apt-get install libav-tool
user@computer:$ avconv -i inputfile.mkv -codec copy outputfile.mp4
Further documentation for avconv can be found here.
Have you tried iDealshare VideoGo which can batch convert MKV to MP4 with no quality loss on Mac or Windows.
Thanks, the above post is specific for Linux based distros.
Useful post