These instructions are for is for showing/hiding a manual on your published site to end-users. You will still be able to see the manual from the Admin view.
Click on the dropdown next to the manual's name
If the manual is already published, then you will have the option to unpublish it. If the manual is not published, you will have the option to publish it.
When unpublishing, all content within the manual will be hidden from users upon they browsing your site, but will still appear in search results unless you also unpublish the chapters and articles within the manual.
When publishing, the chapters and articles within the manual will remain in whatever state they were already in (published/unpublished). You can opt to publish all of the articles within a chapter at once by following the instructions in this article: How to Publish/Unpublish a Chapter
What happens when you do not see unpublish as your admin options?
@Annie - is your site connected to Zendesk? You can't unpublish a manual from Zendesk.