After adding a ".cdc" file to an ISE project, the ChipScope module is still mapped in the design even after deleting the ".cdc" file from the project files.
This is a known issue.
To work around it, clean up the project file when you delete the ".cdc" file from the project files. In Project Navigator, go to the "Project" menu and select "Cleanup project files".
This will be fixed in the next release.