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Delete Action is disabled in WSDL Navigator but Delete action is enabled in WSDL Tree view. There is workaround - choose Refactor -> Safe Delete. But this action doesn't have "delete" shortcut though Delete action from WSDL Tree View Invokes Safe Delete.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss