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This could be a little different depending on which version of the VE you are in. The unmet load hours test and HVAC controls are going to use the set point that shows up for that layer in the ApHVAC system for that layer. Assuming you have them still linked, it would be the same as the master room on the zone.

I'm confused when you say the storage room is inside its acceptable range but the open office isn't even though the open office is the master room. It really should be over cooling or heating the storage room in order to get the office within range.

If you think about it the only set point that a real HVAC system is controlling to is the one for the space where the thermostat is, so the storage room set point can't actually be different.

Based on what you have described about the office not meeting but the storage does even though it is the master room, you need to reapportion the zone airflow in the zone airflow distribution dialog of the ApHVAC system. Give the office more air and the storage room less. The % used for distribution are calculated based on the last room loads results you ad applied to the system.