You don't need to generate anything new at all. You need to individually cut out what you don't want. I assume you'd cut out the ad video, and leave everything else alone.
I had some glitches in a recent project myself, where some video frames repeated themselves (45 frames, to be exact, ~1.5 seconds total). It caused audio to lose sync. I had to demux the audio and video, then drop them both into Womble MPEG Video Wizard. I went and cut out the extra video frames, and then previewed the remaining a/v on the timeline, to be sure there was no more sync issue.
That's all you have to do. You just cut out what isn't needed, don't add more.