This is from my colleague who solved this.
"When Moodle items are made "inactive" or are "hidden" on the main course page a second step is required to make the Gradebook calculations "jive" with the course items.
Following the steps below will change the total course points displayed in the % of Course Completed category.
- After "hiding" items on the course main page, go to Settings > Course Administration > Grades
- In Grader Report select list, choose Full View
- Put a checkmark in the far right "Select" column for all items that are now dimmed ("hidden")
- Scroll to bottom of the page
- In the "Move selected items to.." select list choose "Move to Pretest (NOT Included in grade)"
- Click Save.
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