If you haven't dragged everything over yet to a new project, I am wondering what would happen if you did a 'Save As' for the project, and saved it to a brand new project folder (create the new project folder during the 'Save As' dialog), also checking the Copy All Audio check box, so that all of the audio clips would get copied over as well.
That would be pretty easy to do, and maybe it would somehow correct whatever was goofed up in the project.
I would suggest that if you DO do the above, that you give the project file a new name in the process, to match the new folder name, so that there is no confusion with having 2 project files with the same name.
Worth a shot, I would think, and not much time lost if it doesn't work.
Bob Bone