The large button at the bottom of the page list is used to save the current navigation layout. If any changes are made to the navigation of the course (creating/deleting pages, renaming / rearranging existing pages, changing filenames, changing contribute statuses, etc) you'll need to click this button to save them.
This button will say three things depending on the actions you've taken so far:
The red ‘!’ icon that appears next to the button sometimes is there to tell you that new navigation changes have been saved to the course, either by you or by other users.
Changing settings in the Page tab and Grid settings in the Content tab will also require the navigation to be saved. Elements and interactions that create new parse pages (Convert selection to parse include, tab bar, accordion, etc) will also require navigation to be saved to fully retain their changes.