If there a software solution to fix up a bad mpg video? I recorded some HD content with Mythtv. Unfortunately, The source audio started out with 2 channel audio and then then program switched to 5.1 surround sound. I tried to transcode it with Handbrake, but it fails as the program can not detect the change in audio stream. It tried to trim off the offending bit (it is only about a minute) with dvbcut, but that program only seems to work on standard definition files. It fails to work on HD content. I can play back the original file (but only on certain players - on others the audio track quits after it gets to the 5.1 part or gets wildly out of sync with the video.

Have you tried avidemux? It handles most video. Use it to select the two parts of the video with the different audio formats and split them out into different files. Once you've got the two files, you should be able to convert the audio portion of one to format you want and merge the files back.

Alternatively, you can also try splitting out the audio track twice - once as each format. Convert it to a common format then add it back to the original video.

I would extract the audio, fix it, then merge it back in. It can be done with ffmpeg or mencoder and sox (or maybe faad/faac). Any more info on the specifics, like .mkv format with h264 and AAC or something else ?