Test 1 (on-the-fly correction). Edit DB directly and artificially corrupt the course_modules/course_sections tables with one of the following way: course_sections.sequence contains a module id twice throughout the course course_sections.sequence contains module id and for the same module course_modules.section does not match the section id (note that autofix will think that section sequence is more important!) Edit anything in the course (for example, open /course/edit.php page and save even without making any changes) - this will result in rebuilding the cache and auto correction Make sure debugging messages appear Open DB and make sure that corruptions were automatically fixed. Test 2 (cli script). Corrupt DB as mentioned above or also you can: have an orphaned module (no course_sections.sequence in the course references to it) have some non-existing id in course_sections.sequence Run php admin/cli/fix_course_sequence.php Try running with different arguments and make sure it is understandable what script is doing. Finally run with --fix and make sure everything is fixed in DB.