In the future try posting under the appropriate LEED prerequisite or credit, you will get more traffic that way. Your comment was tagged under EAp2 so that would be the best place. Select LEED Credits, LEED NC 2009, Energy & Atmosphere, and EAp2 Minimum Energy Performance.

Is there a back up system to heat water if the heat recovery system does not have enough output? If so model the baseline system using the same fuel as the back up system uses.

Does Section 6.5.6.2 apply to your situation? If so the heat recovery must be modeled in the Baseline.