What Version of Pepakura Designer are you using ? If you use Pepakura Designer 4 i might be able to help you because you can`t open most of the existing Pep Files in the program itself (i don`t know if anyone else besides me has that problem)
but if you go to your Data Folder where all your files should be stored, try right clicking the file you want to open and then, when the option "Open with Pepakura Designer 4.0.4" appears, click on it and then the file should open within the program.
I hope this hepls you