Hi Joseph ,
You can relink Transcoded files to your assets in encore project. This is a new addition in Encore CS4.1.
Steps :
1. Select the asset .
2. Right click and select Locate Transcoded file ( you can choose from DVD and Blu ray depending upon your project)
This will take you to Transcode folder of project , choose Video and click open , then do the same for audio. Now you will see Transcoding status in project is Transcoded .
Thanks
Minu