When user or teacher marks an activity completion manually,  this means the completion status should override any other rule. If a teacher need to update activity completion settings later, there should be a way to keep status of activities that were marked manually. Otherwise, there is no way to know students for whom activity was marked manually. It's can be time consuming to check logs if there is huge number of students

A solution can be to have a  checkbox in the form so the teacher can decide if they wants to keep manually marked status or not.

Currently, moodle remove the status on the settings update. 

How to test:

1. Create an activity with completion tracking
2.  Mark  manually the completion status for some students
3.  Edit activity completion settings and save
4.  manually marked status are lost.