The trouble with Desktop and Documents enabled for iCloud Drive
MacOS 10.12 Sierra introduced a feature that lets you sync your Mac's Desktop and Documents folder to iCloud Drive. The upside of this is that if you’re not employing any other backup method, all of these files are synced to your iCloud account, and can be available on iOS devices and other Macs.
But the downside is that the feature also automatically deletes local copies of files in these locations if they’re in active use, showing an iCloud download icon on those items, and letting you download them on demand when you do need them. As Apple notes in a support document explaining how to free up storage space: