In the part below, we only want the upper remove extrude faces to be compared in the model. Therefore, we need to remove the unique original faces from the lower remove extrude faces, and add the unique reference faces. The end result will include the unique reference faces of the lower remove extrude faces as part of the unchanged part.
Toggle the View only button to Update.
Right-click in the graphics area to open the Feature Guide and select the optional step Add/Remove.
Select the lower remove extrude faces (to be added) by dragging a selection box over it and exit .
Toggle the Add faces button to Remove faces and select the lower remove extrude faces (to be removed) by dragging a selection box over it and exit .
As can be seen below, with only the unchanged faces displayed, the reference faces have been made part of the unchanged part (marked in gray).
The Reset option undoes the latest face selection.