I add an H.264/AVC clip from my cam, split the audio, ungroup and delete the AAC audio track. I add a new AC3 audio track (the one recorded from the sound mixer to replace the one from the cam). I then render to MP4 file rendering. What I get is a file that is twice the size: the same video back-to-back with the first coming out as expected and the second one coming out with no audio. Where does the second copy of the video come from? It is not in the timeline. What's going on here?

Wow. Very very strange. What versions of ffmpeg, melt and Kdenlive are you running?

I would simply mute the original sound in the clip (small speaker symbol on the left side) then add the other sound track perhaps sync and render.