There is a specific situation where the manual completion button is not able to update the course index.

Steps to reproduce:

1. Create a course in custom sections with two activities (called ONE and TWO) ad enrol a student
2. Enable completion tracking in the course and set the activities completion to manual
3. Login as a student and go to the course page
4. Mark one activity ONE as done (but leave the TWO undone)
5. Refresh the page. This step is important; we want one activity loaded as completed and the other as uncompleted (is the scenario when it fails).
6. In the course index:
   1. Check the activity ONE has a filled circle icon indicating it is completed
   2. Check the activity TWO has an empty circle,e indicating it is not completed yet
7. Mark as done the activity TWO
   1. The course index element icon changes to a filled circle
8. Now undo the completion of activity TWO
   1. As expected, the course index element changes to an empty circle
9. Now undo the completion of activity ONE
   1. Expected: the course index icon should change to an empty circle because the activity is not completed
   2. What happens: the course index icon remains full, no matter the completion state.

It looks like the PHP rendering when the activity is completed does not add some vital attributes, and the JS module cannot update the element.