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The following screenshots both show my iCloud, viewing from Finder and from web. Why some of the folders from web are not there in Finder? May be I deleted them, I'm not sure. Anyway, is it possible to see the missing folders (Keynote/Numbers/Pages/Preview) in Finder?
Go to System Preferences > iCloud > iCloud Drive Options... and check the boxes for Keynote/Numbers/Pages/Preview makes the corresponding folders appear.
Indeed both file explorers should look same:
Apple has this site for iCloud Problem: Get help with iCloud Drive
Several things are described in the link:
If those points are fulfilled and the problem still exists, I would take a macOS recovery into consideration. Recovery is easy with macOS and your files seem to be online and secure as the web browser show the files correctly (About macOS Recovery).
