To open the original and not a copy of the file:
Select the QuarkXPress project in question and doesGet info' from the info window ensure that 'Stationary Pad' is not checked for this project.
This behavior occurs if you have Stationery Pad selected in the Get Info window for a specific project file. The Stationery pad is a function that has been available ever since the earliest versions of the Mac operating system. As described in the Unofficial Apple Web Log, 'If you need to repeatedly modify some sort of a file template, checking this option in any file's Get Info window will tell its parent application to open a copy of it by default, ensuring that the original file remains unedited.'