Karen,
The following code should create you a polygon without Z. Because geometries are immutable, you need to use a geometry builder object, manipulate the Z flag and then obtain a new geometry.
Polygon polygonNoZ = null;
// needs to run on MCT
using (var builder = new PolygonBuilder(polygon))
{
builder.HasZ = false;
polygonNoZ = builder.ToGeometry();
}
However I would also recommend trying to determine which line of code turned your non Z-enabled source data into Z-enabled polygons.
Narelle