Do you have any incremented saves of the project, like MyProject01, MyProject02, etc.?
Do you have any disk or data backups of the project from before the time when you made the most recent changes?
About the only thing I can suggest is to:
1. Do a Revert to Original on all of your transcoded assets.
2. Do a Replace Asset operation on all of your assets that were already DVD-compliant when you imported them.
3. Save the project under a new name, and try building again.
-Jeff
The Focal Easy Guide to Adobe Encore DVD 2.0