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Both MKV and MP4 are container file formats. Container formats define how actual audio, video, subtitle and other data are structured. MKV is an open standard format, while MP4 comes from the ISO and is based on the QuickTime file format.

I don't know Windows, but I have just gone through this in Mac OS X (Linux Applicable). mkvtoolnix is your friend here, and is available for Windows. I used the GUI to check (a sample of) my files to make sure the audio tracks that I wanted to keep and delete were in the same order in the files. Then I manipulated the options in the GUI to match what I ...