I have found that a Premiere CS3 project created and edited in HDV can have surprising behavior on export to Encore, either as a 1440x1080 Blu-ray project or as a 720x480 DVD project. Specifically, even though the total length of the project remains the same, the exact frame locations of some of the cuts or transitions within the project move around.
For example, in a 43-minute project created from a couple of HDV files imported using Premiere, but edited by removing material so that there were many short clips with cuts or transitions between them, a cut about 3 1/2 minutes into the movie was advanced 10 frames, and a cut about 9 1/2 minutes in was advanced about 18 frames. The end of the exported movie was where it should be, except that 3 frames at the very end were black in the exported movie where they were not black in the Premiere timeline.
I suspect this is a consequence of the rigid long-GOP structure of HDV material, although it would seem possible when encoding to regular MPEG2 to start or finish a cut with a short GOP with a new I-frame generated from the original nearest I-frames and the intervening P and B frames.
Can anyone at Adobe or on this forum give a full explanation of just how Adobe Media Encoder handles scene changes in the timeline that take place between I-frames? Does it affect audio sync in any way?