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If you want to delete your fastener connection, use the Delete command in the Intelligent Fastener group.
Then the complete fastener connection is deleted, together with all created holes and added components like washers and nuts.
If you delete the screw with standard Creo delete command, then only the screw is deleted. The holes remain in the parts.
See also:
Deleting Intelligent Fasteners - Creo Parametric 3.0