The correct name for that folder is ~/Library/Mobile Documents/com~apple~Clouddocs, which is also the default view you would receive if you clicked iCloud Drive in the Finder Favorites sidebar item. Basically, Word and Excel are saying they cannot find a previous document that you saved on iCloud Drive.
In System Preferences : iCloud : iCloud Drive : Options… are Word and Excel items selected? If not, the applications cannot see their respective folders on iCloud Drive, and this may be the source of the perceived missing recent documents.
Once signed into iCloud dot com, and just below your name, is a Settings link to a panel that in its lower left, has the means to recover deleted content within a 30-day sliding window. Outside of that window, removed content is gone and not recoverable on iCloud.
My Time Machine backups run every hour that the computer is on, and the ~/Library/Mobile Documents folder is backed up, thus preserving anything on iCloud. Using Dock : Launchpad : Other : Time Machine, I can restore anything from past backups of my iCloud Drive contents, and am not concerned about the 30 day window on iCloud.