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I would write an OpenStudio Measure to remove these orphaned objects. You can run the Measure on your model via "Components & Measures > Apply Measure Now" and see the impact of the Measure before saving the edited model.

Here is the ruby code you to put inside the run method in measure.rb:

# Remove orphaned hot water heating coils
model.getCoilHeatingWaters.each do |coil|
  if coil.airLoopHVAC.is_initialized and coil.plantLoop.is_initialized
    next # Ignore coils that are already connected properly
  elsif coil.plantLoop.is_initialized
    next # Ignore hot water coils that are already connected properly inside air terminals
  else
    coil.remove
    runner.registerInfo("Removed an orphaned hot water coil called #{coil.name.get}")
  end
end    

# Remove orphaned chilled water cooling coils
model.getCoilCoolingWaters.each do |coil|
  if coil.airLoopHVAC.is_initialized and coil.plantLoop.is_initialized
    next # Ignore coils that are already connected properly
  else
    coil.remove
    runner.registerInfo("Removed an orphaned chilled water coil called #{coil.name.get}")
  end
end        

# Remove orphaned water coil controllers (for hot and chilled water coils)
model.getControllerWaterCoils.each do |controller_water_coil|
  controller_used = false
  model.getCoilHeatingWaters.each do |coil|
    if coil.controllerWaterCoil.is_initialized
      if coil.controllerWaterCoil.get == controller_water_coil
        controller_used = true
      end
    end
  end
  model.getCoilCoolingWaters.each do |coil|
    if coil.controllerWaterCoil.is_initialized
      if coil.controllerWaterCoil.get == controller_water_coil
        controller_used = true
      end
    end
  end      
  # Remove unused water coil controllers
  if controller_used == false
    controller_water_coil.remove
    runner.registerInfo("Removed #{controller_water_coil.name.get} because it is unused")
  end
end