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I uncheck Desktop & Documents Folders from iCloud Drive, and I deleted folders manually from Finder, after I copied them to my local storage in my Mac.

The folders size is around 13 GB.

By the time, there is no folders from Desktop & Documents in the iCloud Drive (accessing from devices and the webpage from iCloud), but there is still 13 GB and I can't do anything about it.

Is there any possibility to free up this space?

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    Did you empty the trash before unlinking your Desktop and Documents from iCloud ? When stored in iCloud, the trashed files from those two folders get stored somewhere separate from the main trash. If you unlinked them before emptying the trash, it may have retained the iCloud trashed files, which would still be occupying space. – CJK Mar 4 '18 at 23:24
  • @CJK I did not empty the trash before unlinking them. So, what should I do? It is awful. – Isai Mar 5 '18 at 3:05
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I had to leave this as an answer, because it's too long to explain in the comments section. I'm not guaranteeing that your invisible 13GB of files are definitely hanging around in the iCloud trash, but it's just the most obvious first guess that I could think of. So, let's find out:

Open up Terminal and type in this command:

cd ~/Library/Mobile\ Documents/com~apple~CloudDocs

That will take you to the local storage folder where iCloud keeps copies of your files on your computer. Type ls to list the files in the directory if you're curious, but it's much the same as navigating to your iCloud folder in Finder.

However, what you actually want to do is see if the iCloud trash is still full of files that are taking up space:

du -d1 .Trash

Hopefully, it'll contain about 13GB of files in it. If this is the case, and you're sure there's nothing in the trash folder you wish to keep, just delete the folder:

rm -R .Trash

This is permanent and cannot be undone. So be sure you're happy to lose those files in the trash.

Then type exit and quit Terminal.

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    Thanks for your response. There are no files in the trash folder: the results of du -d1 .Trash, is 0 .Trash. – Isai Mar 5 '18 at 12:45
  • Sorry about that. – CJK Mar 5 '18 at 12:47
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    Thanks a lot! I just liberated 20% of my iCloud space! I would never thought that Mac would synchronize trash with iCloud without any visible way to delete that trash, LoL! – vbezhenar Jun 27 at 18:25
  • Thank you for upvoting, @vbezhenar. – CJK Jun 27 at 22:07
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I'm adding another answer, because there's another possible solution to your problem. I can see from your screenshot that the 13.1 GB of files are categorised under Other Documents.

I navigated to the same window in System Preferences to get more information on this. When I click on Other Documents, a description appears in the right-hand pane:

iCloud Storage on MacOS

Perhaps this is too obvious an solution to be worth any merit, but have you opened up your iCloud folder in Finder and had a look at the files sitting at the top-level of the folder ?

In case you don't know how to open the folder in Finder, go to Finder, and either access it from the menu by selecting Go > iCloud Drive, or press the keyboard shortcut I.

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I was able to free up space by going to icloud.com, clicking on "Recently deleted items" in the lower right hand corner, and deleting what's there. Note that it seemed to have some trouble with large directories. It would show them as deleted, but they would still be there after reloading the page. For some reason, it helped if I left the page open until it didn't warn me about navigating away from the site. Eventually I got everything purged and my storage space was freed up.

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It seems that macOS 10.14 Mojave has no permissions settings for the ~/Library/Mobile Documents folder. None of these files appear in the iCloud web interface or under recently deleted/recover file.

I had no "Other Documents" setting in the iCloud Manage Storage Preference Pane and after disabling all apps in iCloud, there were still files in the folder. I had to completely shut off the iCloud service in order to remove the files.

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