Existing building, two parts, only one certified

I am going to model an existing building that is being altered. The situation is as follows: A. The building is divided in two parts, one (offices) is going to be certificated LEED, the other one (factory) isn’t, although both are being altered. B. The HVAC plant is partly common to both sides (a boiler and a heat recovery system are common), but the certified part could be conditioned also without the common HVAC part, because both cooled water and heated water can be provided by a heat pump that is dedicated only to the offices. I have two doubts: 1. Shall I model both parts? If the answer is affirmative, in the baseline model for the envelope shall “the baseline building design reflect existing conditions prior to any revisions that are part of the scope of work being evaluated” for both sides? Could the part that is not certified be modeled in a simplified way? 2. When Table G3.1 5.f. states “existing conditions”, does it refer only to U-values and to SHGC or also to dimensions of glazed surfaces or to distribution of the zones (internal partitions are being moved during the refurbishment work)? With Regards