Question-and-Answer Resource for the Building Energy Modeling Community
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You will probably get a whole pile of unmet hours by changing the availability, which for an existing building is probably realistic, but will be a problem if this is a LEED model. You can address that by changing your heat/cool setpoints to reflect the availability of each system (i.e., change the heating setpoint to 50F during your cooling season).
For what it's worth, I had a dorm project with 2-pipe fan coil that I modeled both as a fan coil system per zone and a system for the whole building, just for grins, to see the difference (easy to play with right out of the wizard) -- and there really wasn't a difference in results. It worked well both ways. I ended up doing one big system just because it is easier. Just be sure you calculate the fan power correctly either way. Set OA to zero at zone level (exhaust at zero too) and it should not be a problem.
Good luck!
