Baseline Shading System

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Get a copy of the ASHRAE 90.1 vintage you are using in your LEED certification. Consider also getting the User's Manual that goes in pair with it.

ASHRAE 90.1-2010 (but same in 2007 and 2013 as far as I remember), Table G3.1, Section 5. Building Envelope, Baseline Building column:

f. Existing Buildings.

For existing building envelopes, the baseline building design shall reflect existing conditions prior to any revisions that are part of the scope of work being evaluated.

I would model it as per the baseline building, so included an unconditioned zone that will serve as your roof cavity, or whatever is actually the case.