Mac OS now has a feature that sounded convenient where it automatically moves files in your user folder, including Documents and Desktop, to iCloud. Notice I said “moves” not “copies” because I found out the hard way that it is not copying like a backup. It is moving your files to iCloud and will eventually (within days) delete the files from your local storage. This is an absolute nightmare for my workflow where I keep my working files in /Documents/Freelance/ClientX/ etc. I opened a project that I hadn’t worked on for a couple weeks to find everything was offline. MacOS had deleted all the media files from my local SSD and Flame couldn’t see the files that the Mac was linking to from iCloud.
The short term fix is to explicitly tell the Finder which folders to download from iClould but the permanent fix is super annoying and a little scary: you have to go into System Preferences and tell iCloud not to manage your User folders. It then deletes all those entire folders from your SSD and you have to download everything from iCloud. This was over a TB of files for me. This only really applies if you put any important stuff in your user folder. If you’re using an external drive, I don’t think this has any effect. The super crazy thing was that this was on by default when I got my new computer. I assume that’s the case for all Catalina users.