Lost Files in iCloud Drive App Folders

Hi there! I’m facing an issue where the app folders for Numbers, Pages, Keynote and Shortcuts have been emptied within iCloud Drive . Other folders (both those created by non-Apple apps and those created by me) in iCloud Drive are unaffected. As I remember, the files included Pages, Numbers, Keynote, PDF and JPG files.

The files missing are not in the recently deleted folder. They also do not seem to be present in the recover files section on iCloud.com, however the recovery tool states there are exactly 5000 files available to recover. Perhaps there is a limit to how many files can be shown or are kept available to recover? I can’t recover the files to remove them from the recovery section as I get an error when I try. That’s just a theory on my part though.

The files do not appear “On This Device”, in any recently deleted folder, or on my iPhone, iPad, iCloud for Windows 10 app, Windows 10 recycling bin or on iCloud.com.

I noticed the files were missing a few days ago after I did a clean installation of Windows 10 on my PC, installed the iCloud for Windows 10 app, synced the iCloud files and copied approximately 40GB of files from Google Drive to iCloud Drive on Windows 10 and selected to skip files which were already present in iCloud Drive. I did this so I could stop using Google Drive and use iCloud Drive as my only cloud storage.

I have contacted Apple Support and they did some checks and told me to check through the 5000 files in the recovery section on iCloud.com for the missing files and contact them again if I didn’t find them. I will be getting back in touch with them tomorrow as they are not present in the recovery section.

Does anyone have an idea as to how this happened and or how I can recover my files? It’s certainly very strange and frustrating behaviour. Thanks for any help!