CLR Flush

Another question.....

This winter I'm planning on pulling the dash apart to repair gauges, replace the radio, replace the wiper gaskets and bushings and service the heater and vents. When I'm finished flushing, I'm planning on bypassing the heater core so I don't have to drain the system in the middle of the winter. Am I missing something? Can the heater core be left for the winter without fluid in it?
I don't think it'd hurt it. If water was left in it over the winter, you might experience it freezing and bursting.