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To delete a folder, the folder needs to be empty. This means that all three folders: documents, media and models need to be empty.
If you get a meassage that the the foldes can not be deleted because it is not empty, check that there is:
If there are content in any of these, you need to move or delete that content.
The folder need to be completely empty before you can delete it: no documents, no media, no flow models.