In case anyone is following this or has the same problem, I worked it out. In the schedule, under "Apply Format Options to: Preview" I did not have the "Enable Object's Pen" box ticked, therefore all the lines were displaying in the contour pen selected. The implications of this are not apparent until the schedule is placed on a drawing as the hidden lines are still hidden in the schedule but appear in the drawing.
Another issue this raises is that, when the "Enable Object's Pen" box is ticked, the schedule does not actually reference the objects pens. It references the pens selected in the object's Selection Settings - Floor Plan and section - symbol and outline pens, even if the "enable objects pens" box is ticked here.
This is really annoying and cumbersome, but at least my issue is solved.
Kathryn
Archicad version 19
Windows 10