The Unitary HVAC Design Heating Capacity and Unitary HVAC Design Cooling Capacity options that you're using are internal variables -- items that are set once at the beginning of a simulation and don't change (zone floor area, sizing results, etc.). That's why they're not working to dynamically change the coil capacity. To do that, you should instead use actuators. EnergyPlus only has a specific pre-defined list of actuators that you can change -- you don't have the capability to change ANY detail of the model. For cooling coils, it looks like the only actuator available related to capacity is specifically for autosized capacity of single speed DX coils. There don't appear to be any options for actuators related to capacity of heating coils.
There are two workarounds that you could explore to "force" the coils to provide a specific capacity -- the actuators for node setpoints (flow rate, temperatures, and possibly humidity) and the actuator for the performance curve results.
You can read this post for more details.
