Media files exist but MyCloud share containers have disappeared

[cpt_paranoia]

Right, it sounds like you have the ‘vanishing shares’ problem; there were other reports of this, and permissions problems:

http://community.wd.com/t5/My-Cloud/Folders-Within-Public-Share-Read-Only-after-Firmware-Update/td-p/902536/page/16

http://community.wd.com/t5/My-Cloud/Loss-of-Access-to-Shares-with-Firmware-v04-04-00-307/td-p/901585

http://community.wd.com/t5/My-Cloud/cannot-see-shares-after-update-04-04-00-308/td-p/907322

http://community.wd.com/t5/My-Cloud/Missing-Shares-Preventing-Safepoint-Update/td-p/906190