I found out today that FFMPEG doesn't support FLAC files in the audio stream so remuxing isn't an option. If you try it you'll get the following error:

Could not find tag for codec flac in stream #1, codec not currently supported in container Could not write header for output file #0 (incorrect codec parameters ?): Invalid argument

Fortunately, it does support h264 audio stream, so all you need to do is to re-encode your audio like this:

ffmpeg.exe -i Sample_Video_File.mkv -vcodec copy -acodec aac -strict experimental -ab 128k Converted_Video_File.mp4

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