Working on a cs3 PPro project, going very well! Updated to SC4 to take advantage of its improved 3D modeling capabilities. However I note that now my sc3 project, once set up in cs4 is now out of synch. Edits aren't where I placed them - I assumed you could transfer cs3 to cs 4 no problems.
Normally, CS3 Projects do translate to CS4 Projects well. General wisdom is to complete in the version that was used to start, but I see your point on wanting to move up here.
Maybe give the specifics of this Project and its Assets, as there could be something there.
Also, did you Open the CS3 Project into CS4, or did you Import it. Might want to try the other way, depending on what you did.