Are the files missing when accessing that folder/Share using Windows File Explorer or Mac Finder?
What web browser were you using to access MyCloud.com? You could be experiencing the issue others are when using MyCloud.com where not all folders are shown. As a test, try using a different web browser.
Here is one recent thread on the missing folders…
http://community.wd.com/t/not-seeing-all-my-files-and-folders-in-mycloud/142558/
