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1. Copy the file sites/all/modules/ckeditor/ckeditor.styles.js

2. Paste it into sites/all/themes/mycustomtheme/js/

3. Edit the list

4. Tell CKEditor where to look for this file: admin/config/content/ckeditor -> choose text format -> edit

5. Under the CSS tab: Predefined styles -> choose "define path", then: Predefined styles path: %t/js/ckeditor.styles.js

6. When changed, and no changes visible, change the path to %t/js/ckeditor.styles.js?v1, %t/js/ckeditor.styles.js?v2...

Example: Erik Rydberg website