My boss finished a video he was doing in Premiere and dynamically linked it over to Encore but now it seems that most of the video clips he was working with are gone. I know when you first start an Encore project it asks you to specify an empty folder. Is it possible that he chose a folder filled with the video clips he was using and Encore deleted them? He's one of those guys that clicks "yes" without fulling reading the warnings sometimes so that's my guess as to what has happened.
Does Premier still see the videos? If the videos are truly missing and you restart Premier the software should ask you for the video file locations.
Encore can overwrite files like the DVD ISO file but but it will ask you for permission.
What Encore output are you creating i.e. DVD, DVD ISO, DVD Folder? Be fore warned that DVD Folder output should only be used for Encore generated files. Do not place anything in the specified "DVD folder" that you don't want deleted. The first step in DVD Folder creation is to remove everthing under the folder. So incorreclty pointing the DVD Folder to the wrong location could have disasterous results.