There are also tools like MP4Box which can also create MP4 containers - the same exists for MKV with MKVtoolnix. You can swap containers easily with FFmpeg – you just have to tell it to copy the video and audio streams: ffmpeg -i input.mkv -c copy -map 0 output.mp4 This doesn't lose quality, and it'll be a much faster process. Since passthrough is not possible, ask yourself: Do I need to re-encode? If you only want to change the container from MKV to MP4, you usually don't need to encode anything, you just change the 'wrapping' around the video. Do I have to re-encode? Couldn't I just swap the container? So, anytime you're changing containers with Handbrake, your video is going to get re-encoded, which means it a) takes time and b) may introduce quality loss. HandBrake is designed to be a video transcoder. Sorry, adding video passthrough is not planned. See also the respective feature request that would have enabled video passthrough: MKV to MP4 in your case), Handbrake will re-encode the video.
When you're using Handbrake to convert from one container format to
