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I now have the exact same behavior on two Macs--Documents, Desktop, and Downloads are present but no other iCloud Drive folders.
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On my Mac I have Documents, Desktop, and Downloads in iCloud Drive but all the app-specific folders are gone. No issues on iOS.
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Yes, this also worked for my 2015 iMac. I turned off iCloud syncing for photos and just deleted the photo library--I personally don't mind doing this because my Photo library is also locally saved on a non-Catalina server Mac, which in turn is backed up to Backblaze, but I agree that if your photo library in Catalina is the only local copy you have you should absolutely not delete it.
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I set the computer to stay awake and it keeps happening, so it must not be a power saving thing.
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apart from the issue with fans, this sounds the same as the bug that I have, but with an iMac. https://forums.developer.apple.com/thread/120716
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Simialr issue after Catalina Beta 4--PHPhotosErrorDomain error 1000. Photo Library starts updating at 79% and fails at 100% with that message. The backup photos library some documentation references was never created.
