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Why change programs during a project? The golden rule is to finish projects in the program you started it with.
But having done in it anyway ....?
The first suggestion is to use the last auto save from CS3 to finish it in CS3. And to be honest, I don't have a second suggestion.
Happened to me with a P2 project. Because there was no 24p P2 preset anymore it came in under a desktop preset at 29.97 (wrong frame rate). To fix it, I copied and pasted to a new sequence with the correct preset and 'interpret footage' and it all worked fine.
Even if you didn't shoot 24p, try it. Make a new sequence in your project then copy and paste the clips into it.
Sadly, this is not the case for me. The timelines are new in the CS4 version, but the footage from the CS3 Project still has the yellow render bar. And if I import the same MXF clip into the CS4 project and put IT on the timeline - it's fine. Even footage from the CS3 project that is offline and then reconnected has the yellow bar. Even when you chose to "replace footage" with the same clip, the yellow bar stays. So there is something that CS3 has written somewhere to indicate how the footage is supposed to be decoded that I can't get rid of. Replacing every clip seems to be my only option. Interestingly, when I do that, the program uses the same conformed audio files - so that's some good news.
What frame rate did you shoot? And what resolution?
4 Mono Tracks
5.1 MB/Sec Avg
I don't understand man. The only thing I can think of is maybe the footage was shot 24p on a 60i stream. If that's the case you need to 'interpret footage' and check the 24p box for all the clips. CS3 did it automatically but you have to do the work around on CS4.
Was the camera set to 720 24p or 24pn. If it's not 720pn then the 'interpret footage' is something you have to to do.
Does that make sense?