I use virtualdub for this but it kinda works best with AVI extensions. Highlight all the track and dub it in a video direct streaming mode but with the audio encoding option as "none" or equivalent (don't remember what it was called)
You can then direct stream copy the audio-less video dubbing the new track on it.
Don't remember where specific option are, but the above can be done with virtualdub natively.
The last time I used it, it was a free software.
I confused you with another member called Strollen (if I get the spelling right)