Thanks for asking. We don't flush engine, generator, etc after every use. When we do flush things in fresh water depends. For example today we are at Renaissance Marine (very nice, BTW) in Aruba and are here for 6 nights. After we arrived we flushed out 1)Yanmar, 2)Anchor Wash Pump, 3 and 4)both toilet pumps and circuits-we use fresh water flush when we have dock water and 5)generator was already flushed 6) AC all 3 loops 7) the distribution manifold which is flushed end to end along with the other items and 8) the strainer itself.
Fresh water can 1)reduce corrosion which is higher for salt water than fresh water 2) reduce galvanic action by minimizing the salt water connection to AC and feed pumps, etc or dissimilar metals 3)minimize and stop--even kill marine growth and 4)help to dissolve deposits that might be forming--RO water in particular is good at this, and 5) reduce rubber hose odor and aging.
Our Yanmar for example has the following items that are cooled directly by salt water--1)transmission cooler, 2) turbo intercooler, 3) oil cooler 4)coolant loop and 5) raw water pump and impeller and 6)exhaust elbow and exhaust hoses.
Is it necessary? Decide for yourself. I do know that Amel owners use Barnacle Buster and other harsh products because of overheating problems, there have been leaks from the oil cooler into salt water necessitating a oil cooler replacement, generator impellers fail and their salt water pump faces have to be sanded, end caps for generator heat exchangers corrode, feed pumps have needed rebuilds, and water manifolds have corroded. Also, owners have needed to clear marine growth from the manifold and the strainer. A lot of this stuff is shown in Bill's manual. In fact if you have any doubts about the impact of salt water just thumb through that manual.
Like other owners with solar and those with wind chargers, or both....we only run the generator infrequently, usually to make water and we have about 5 days to a week of time on average between runs--but at anchorages we have gone as long as 6 weeks before needing to run our generator. We have enough solar to run our HW heater 30 minutes and still top off our batteries to float. We usually run our clothes washer while making water but it can also be powered by our inverter underway when we run our engine. Just de-anchoring and departing an anchorage can require a 30 minute engine run and the fast cycle on our Thompson takes 30 minutes. We use the standard yellow Xantrex 1800 watt pure sine inverter.
Not trying to brag about our solar capacity, but pointing out that many owners can have long periods of non-use of the generator when anchoring, and of course at a marina.
Procedure--Flushing systems with fresh water is very quick and easy to do. It sounds involved when describing or discussing it but it is super-simple and quick. We just close the ball valve inlet for the strainer, open the cover (this is done anyway to check strainer after a trip or generator use) start the device and use a hose or jug or both if your hose can't keep up. . If you want to make sure you have removed most salt water from the strainer and inlet you can pull fresh water through the toilets or anchor wash before starting and flushing the generator. Usually we have enough jug water (we have 3-8 litre jugs) to do the entire process. Good shore pressure water lets you do it with just hose alone....at anchor you can use a combo of cockpit shower hose and jugs but usually we just pour water into the top of the strainer using a jug....easy to keep up and to avoid over filling. Flushing the generator is a single person operation. Flushing the engine, toilets, AC and anchor wash is best done by people.
I am sure that it can be done safely, but IMHO there are some risks to plumbing-in a fixture--pressurized water can be forced through the salt water cooling path into the lift mufflers which will fill and then water will climb to to the top of the exhaust loop. Because our exhaust loops are up high, higher than the exhaust elbows of our generators and diesels, there is a risk of backflooding those. I'm not saying that a plumbed in approach is wrong, but I would pay attention to design and very close attention to operation--we just use the open strainer top method. It is also possible to supply the water from the 3 way flush valve for your watermaker but we just use hose and/or jugs.
A final note, if you are needing to replace an impeller or do any other work on a salt water circuit, run fresh water through it first. The water you spill over other things in your engine room will be fresh rather than salt.
Bob and Suzanne, SM KAIMI