Are you sure he is talking about the raw water side? That sounds more like an engine block freshwater side cleaning process. The Onan raw water system is really simple and can not be setup to recirculate while running.
A pump, hoses, heat exchanger, and exhaust elbow. It is also not made of things that "rust". The pump is bronze, and the heat exchanger is copper-nickel. They can corrode, if the zinc is not maintained, but they typically do not clog from this, they just get thinner. The can clog from biological fouling if run a lot or from salts precipitating from seawater if not run often.
The exhaust elbow can not be cleaned effectively in-situ, it really needs to be removed if it is clogged or fouled.
The only process I know of to clean in place requires removal of the pump impeller, then pumping a phosphoric acid based cleaner (like BarnacleBuster) through the pump and heat exchanger. This bypasses the exhaust elbow, and is effective, but does not involve running the engine at all.
The Onan system is simple enough, if my heat exchanger was in need of serious cleaning, I’d take it off and clean it by hand.
Fort Lauderdale, Fl, USA