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This is because different user credentials are used to log on in with FTP and cPanel, and the file operations done by Apache in executing the PHP scripts. The file ownership and permissions decide if deleting is allowed or not. When files or folders are created by Apache (php), it may be that you can not change it from cPanel or FTP. It has to be done with a File manager from within XOOPS, altough I had once with some folders from Formulaire, which appeared unchangable that I had to open a ticket for it.