If you take the end caps off the heat exchanger, you can see the tubes the raw water flows through. Flushing and replacing the coolant does not touch the inside of these tubes. To truly clean out the heat exchanger you need to remove these caps. I stuck mine in a tub of hot water and detergent, which worked OK for mild cleaning. I could seen into the tubes and there was nothing but a little slime. More robust measures are needed to remove scale and barnacles. Back in the day it was common to get car radiators boiled out at a radiator shop. If any shops are around that still do this that will clean a heat exchanger too.
Joe Coquina
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