I know this is fiddly, but it's a recurring pain point for people at institutions where admins have added a bajillion additional buttons to the course-level nav.
Please move the location of the Save button for the course Navigation tab in the Course Settings to the space between the list of things that are shown and the list of things that are disabled.
When there are enough items in the Navigation list, the Save button disappears off the page. Because people don't use this interface all the time, it's easy to forget that there's a Save button. It's one of those weep-worthy things when you've just clicked to disable 20 things from the list to make it actually usable, and then you forget to scroll to the bottom and click Save. Putting the button in that middle space will make it more visible and memorable, even though it makes the placement inconsistent.
Here's a screenshot from an institution that has almost nothing additional added, and even then, the button is getting close to disappearing.
Here's an illustration of what it's like when you have more buttons to contend with: