The Directories->Delete->Confirm menu item is a toggle for the delete directory confirmation. This option is also available as an option on page 2_2 of the Settings notebook.
When the Confirm option is enabled, there will be a two-step confirmation, first the Delete Directory Confirmation dialog. If choice of that dialog is to delete the directory, a 'last chance' confirmation appears.
When the Confirm option is disabled, only the 'last chance' confirmation appears.