On My Cloud Home, the Windows network share and the files shown through MyCloud.com are not necessarily the same view, and WD specifically notes that local network access is separate from the web/mobile interface. Also check whether the missing files or folders start with . or ~ because those are hidden from the web interface but can still appear locally. If neither explains it, compare the exact folder path and user account on both sides before doing anything destructive.
Thanks, I thik I found the problem. One of the hard drives appears to be defective.
