I have flushed my heater core as regular maintenence every two years, and my heater core is still fine, This is on an '88, so flushing wont ruin your heater core, not maintaining your system will do it.
And if you flush your system, Flush your heater core seperately at first and the radiator seperate, then when they are both clean hook everything up and do a backflush with chemicals and you will not have problems and your cooling/heater system will out preform your expectations.