To activate this you need to have Sensei installed and must be logged into admin. Next add the code below to your functions.php file. Then go to: yoursite.com/wp-admin?sensei_update_user_course_data=start

functions.php

add_action('admin_init', 'refresh_user_course_completion_data');

function refresh_user_course_completion_data(){

    if( ! isset( $_GET['sensei_update_user_course_data'] ) ){
        return;
    }

    if( 'start'== $_GET['sensei_update_user_course_data']  ) {

        //enqueue the scripts needed
        wp_print_head_scripts();
        wp_print_footer_scripts();

        echo '<h3>Update user course statuses </h3>';

        $url = get_admin_url() . '?sensei_update_user_course_data=go';
        echo '<a class="button" href="'. $url . '" style=" background-color: green; color: white; padding: 0.5em 1em;
" >Go</h3>';

    } elseif( 'go'== $_GET['sensei_update_user_course_data']   ){

        echo '<h4>Updating all user course statuses...</h4>';
        echo '<h4>--------------------------------</h4>';

       update_all_user_course_statuses();

        echo '<h4>--------------------------------</h4>';
        echo '<h4>-- Update completed thank you --</h4>';

    }else{

        return;

    }

    die;
}// end refresh_user_course_completion_data


/**
 * process all course sna update the users taking the courses status
 */
function update_all_user_course_statuses( ){

    cust_print( ' Retrieving courses...' );
    $courses = Sensei()->course->get_all_courses();
    
    cust_print (' Retrieving all user taking these courses...');

    foreach( $courses as $course ){

        cust_print( 'Updating users for Course:'. $course->post_title );



        cust_print('>> retrieving course users...');
        //get users taking this course
        $args = array( 'post_id' => $course->ID, 'type' => 'sensei_course_status' );
        $user_activities = WooThemes_Sensei_Utils::sensei_check_for_activity( $args , true);

        //get user ids
        $user_ids = array();

        if( !is_array( $user_activities ) ){
            $user_activities = array( $user_activities );
        }

        foreach( $user_activities as $activity  ){

            if( !get_userdata( $activity->user_id  )  ){
                //ignore invalid users
                continue;
            }

            $user_ids[] = $activity->user_id ;

        }

        if(empty( $user_ids )){
            continue;
            cust_print('>> no users in taking this course');
        }

        // lop through users and go through each of the lessons on the course to check if they have
        // completed it
        foreach( $user_ids as $user_id ){
            complete_user_course_when_all_lessons_complete( $course->ID, $user_id );
        }
    }

}// end update_all_user_course_statuses

function complete_user_course_when_all_lessons_complete( $course_id , $user_id  ){

    $user = get_userdata( $user_id );
    $message = '>> Processing '. $user->display_name . ' ... ';

    $all_course_lessons_completed = true;

    //get course lesson
    $course_lessons = Sensei()->course->course_lessons( $course_id );
    foreach( $course_lessons as $lesson ){

        if(  ! WooThemes_Sensei_Utils::user_completed_lesson( $lesson->ID, $user_id  ) ){
            $all_course_lessons_completed = false;
            break;
        }

    }

    // what is the users current course completion status?
    $current_user_completed_status = WooThemes_Sensei_Utils::user_completed_course($course_id, $user_id);

    // update user status if the lessons are complete but the course is not
    if( $all_course_lessons_completed && ! $current_user_completed_status  ){

        WooThemes_Sensei_Utils::update_course_status( $user_id, $course_id, 'complete' );
        $message .= ' course completion updated';

    }

    cust_print( $message );

}

/**
 * Custom printing function for this update script
 * @param $string
 * @param string $tag
 */

function cust_print( $string, $tag="" ){

    if( empty( $tag ) ){
        $tag = 'p';
    }
    echo '<'. $tag . '>';
    echo $string;
    echo '</'. $tag . '>';
}

Which function.php file? in the theme function.php file?

@dairdr If I'm reading this correctly, this is meant to be ran once to update course info. So, if you want, you can add it to either your parent theme's functions.php or your child's functions.php. Run it once by visiting the url mentioned above. And then you can delete the additional code.

Hope that helps!