Exported DXF file has diagonal lines that alter the surfaces

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I assume you are using the EnergyPlus Output:Surfaces:Drawing object to generate a DXF file at run-time. The default behavior for Field Specification 1 field is "Trinagulate3DFace". You can change this to "ThickPolyline" or "RegularPolyline" and then the surfaces won't be triangulated.

This doesn't affect the simulation results, just the dxf file that is created along with the simulation results for visualization purposes. This EnergyPlus feature pre-dates the SketchUp plugin when modelers would inspect the dxf files generated by EnergyPlus.