How are you backing up the computer and mobile phone? Using what app or software? Are you using WD Sync?
Windows File Explorer is typically what one would use to search their My Cloud Shares to search for files.
Yes it is a bit complicated to use SSH to access the My Cloud to see if there are hidden folders not being shown when one uses Windows File Explorer.
One can erase all user data on their My Cloud and reset the device to factory default by selecting Quick Restore in My Cloud Dashboard > Settings > Utilities > System Factory Restore. It is suggested one backup their My Cloud prior to performing a Quick Restore. One can use the embedded My Cloud Backup/Safepoint feature to backup a My Cloud to a USB hard drive attached to the My Cloud USB port, or manually copy the files on the My cloud to another location. Note Full Restore takes a very long time as it securely erases the user data on the My Cloud.