Select the checkbox Do not show this warning again. Once you have done this, no alert will be displayed for projects that are opened twice.
Additional Notes:
If you want to restore this alert, click on the Show all Alerts button in the Display preferences for QuarkXPress.
Macintosh: QuarkXPress > Preferences > Application > Display > click Show all Alerts (Button)
Windows: Edit > Preferences > Application > Display > click Show all Alerts (Button)