Replacing MP4 Tracks

First, the replacement track

mkvextract tracks Phantom.mkv 1:Phantom.ac3
sudo ffmpeg -i Phantom.ac3 -c:a libfdk_aac -vbr 5 Phantom.aac

Then the removal and addition (this keeps the Handbrake added chapters, subs and what not. You could remux alltogether if you wished)
MP4Box -info someVideos.m4v
MP4Box -rem 2 someVideo.m4v
MP4Box -add someNewTrack.aac someVideo.m4v
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