Background:
In some users' workflows, custom Color Output setups (Edit > Color Setups > Output) are used for display of projects and also used for print / create PDF. When these projects are opened on different machines, where QuarkXPress has different preferences settings; then custom Color Output setup cannot be deleted by going to Color Setups > Output (in Default Output Setups window)
Solution:
1. Open the project in QuarkXPress
2. Navigate to Utilities > Job Jackets Manager (Job Jackets Manager window opens)
3. Select the Project Job Jacket (on left hand side) and Output Setups on right hand side
4. Select the custom output setup and delete it using Trash button as shown in below screenshot:
5. Click on Save.
6. Save the project, close and reopen the same.
Note: Sometimes it does not allow you to Save the project, In that case you need to select Save As.