Which is the best way to go from MKV to MP4?
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Do your files have any specific mkv features you want to keep ?
Yeah, ffmpeg is definitely a good option.
If the MKV contains video and audio supported by the MP4 container, you can remux as an MP4.
AnotherGUI is a handy GUI for that sort of thing. You can drag and drop a bunch of files onto it and let it run. An AnotherGUI preset for copying the video and audio from any ffmpeg supported format to an MP4 looks something like this:
-i "<FullSourceFileName>" -y -threads 1 -vcodec copy -acodec copy "<OutputPath><OutputFileName>.mp4"
If you wanted to copy the video while converting the audio to AAC:
-i "<FullSourceFileName>" -y -threads 1 -vcodec copy -acodec aac "<OutputPath><OutputFileName>.mp4"
I think I use -threads 1 because AnotherGUI can be configured to convert more than one file at a time.
So you know, the current version of AnotherGUI (2.3) checks for an update and reports there is one, but the update it finds is an older version. I've reported the bug to the author, but it's no big deal. It just shows an available update on the title bar you can simply ignore.