Audio Files Vanished from Logic Studio Project

I bounced a project. Created a new project to do some mastering. Imported the bounce track and mastered it. When I went to quit the application is asked me if I wanted to copy over the audio files. I wasn't sure why it would ask that since I imported the audio files that I wanted. It went and copied the entire folder of audio files into the mastering folder, but a bunch of them have vanished from both folders. Now I have these blank spots in my arrangement where the vanished files used to be. They are not in the trash or anywhere else on the drive. Can anyone tell me what the heck happened?