Sometimes we find activities that exist but not being displayed on the course/section page. The reason they are not displayed is that their id is not present in the section sequence. Running the admin/cli/fix_course_sequence.php CLI on that course id fixes the issue and activities become visible. We spent some time desperately trying to figure out how these activities become broken and how their ids get deleted from the section sequence but no luck unfortunately.

The CLI script admin/cli/fix_course_sequence.php was implemented as part of MDL-37028. There probably was a reason to implement it and it looks like the reason is still there.

It would be good to fix the root issue and then deprecate (remove) admin/cli/fix_course_sequence.php CLI script.

Originally the issue was observed in 3.9 moodles but it still exists in 4.1.