Exporting files with AC3 audio

Forgive me if this is not the right place to post this question.
Using QT Pro, I want to trim and edit some files containing AC3 (Dolby Digital) audio. When I export or save the edited video, will they retain the AC3 audio?
More specifics: These files contain both AAC audio (in the default track) and AC3 audio (second track). These files were encoded using Handbrake, and I will be playing them on my AppleTV (hence the desire to retain the AC3 audio). The source files come from my DVR, and I want to trim some commercials. I tried to trim them prior to encoding, but I'm having trouble finding reliable software for editing MPEG2 streams on a Mac. Thus, I'm trying to figure out whether or not I can trim them afterwards using QT Pro and still retain the AC3 audio.
Any thoughts would be appreciated. Thanks!

Aaah, I wish I could help! I have exactly the same problem! I was going to post about it, but since there's this workaround, I didn't want to take up bandwidth with a problem that was not a total showstopper.
Indeed. I have stopped doing what I used to do before. Before, I used to select "All" in compressor - the files generated were the video, the aiff, and the ac3. Well after burning a few coasters through DVDSP 4.1 where there was picture but no sound, I realized that I needed to drag the aiff file to compressor again, and use that - at that point everything is fine. So, right now, my workflow is to export just the video from FCP through compressor, let it encode. Then export the aiff separately and encode it to a3 in compressor, then import the video and ac3 to DVDSP for good results. In short, no more exporting "All" from FCP through compressor, it's a waste of time.
But as to why, I have no idea, and I'm eager to hear what folks have to say! Anyhow, just letting you know you are not alone. Btw. my set up is: FCP 4.5 HD, compressor 2.1 and DVDSP 4.1.0... what's yours?

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