I've got an HD MPEG-2 and a Dolby 5.1 AC3 in Encore for output to Blu-Ray. However, it's only outputting a stereo audio track. The client had added some title slates to the front end of the project, lengthening the video track, without lengthening the audio file. I had to manually find a synch point in the audio which synch's up and starts at about 28 seconds in to the video.
My question is, since the audio and video aren't 1-to-1 for the entire length of the piece, is that causing Encore to decompress the AC3 file and re-render it to the length of the video file?