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I created some ruby code that finds all the EMS objects in the model and removes them. These objects were indeed getting "stranded" and needed to be removed through house cleaning (in this case, through a ruby script) for the simulation to be successful.
Ruby code was written that removes all EnergyManagementSystem Sensor, Actuator, GlobalVariable, Program, Subroutine, and ProgramCallingManager objects from the model.
The script snipping above finds all EnergyManagementSystem:Sensor objects in the model, and stores them in an array ems_sensors. That array is iterated through, and each individual sensor is removed using the .remove method.
Similar lines were written for the other EMS objects (Actuators, Global Variables, etc.)