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I would recommend adding the "Zone Thermostat Heating Setpoint Temperature" and "Zone Thermostat Cooling Setpoint Temperature" output variables to confirm that thermostats are defined correctly. The setpoint manager may be controlling the temperature from the outlet node after the reheat coil or terminal, which is technically the inlet node to the zone -- not the air node for the zone itself.
No, the "Unused Non-Parent Object" message in the SVG file shouldn't cause you issues in terms of simulation results or accuracy. @jason_glazer should confirm this since he wrote the HVAC-Diagram auxiliary program that converts the BND file (branches and node connections) into the SVG file that shows HVAC diagrams. The HVAC-Diagram auxiliary program has a preset list of objects that it looks for in order to build the HVAC diagrams (see the table in this link). If an object in your IDF isn't part of that list, then it shows as an "Unused Non-Parent Object" at the bottom of the SVG file (source code for where that message is generated). This message has no impact on the EnergyPlus simulation itself -- just the SVG diagram.