The de-rating option in PV Elite applies mainly to flanges on the end of nozzle necks attached to piping. There is a check box at the lower right of the 1st window of the nozzle dialog you must check the box to alert PV Elite to go through the procedure outlined in Code Case 2901.

This option does not apply to body flanges on heat exchangers and similar types of equipment, only nozzle flanges.