The additives in the coolant prevent rust from forming. If the coolant is not changed on schedule the additives no longer prevent the formation of rust. If you have fresh coolant you just have to worry about existing rust. There are some products by prestone and others designed to loosen rust prior to a flush.

If your heater core is partially blocked you need to make sure it is reverse flushed so the rust is pushed back out of the core not further into the core were it may be trapped and later lodge itself again
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Paul NW Indiana '89 740 Turbo 110,000