For what it's worth (my engine is an old Volvo MD30A) I always flush out the raw water system - particularly the heat exchanger
- with fresh water when checking or replacing the anode. I don't know how you'd do it on your engine, but I simply remove the pipes from the back of the heat exchanger
and flush through with a hose against the normal raw water flow, allowing the water to drain out through the other end of the heat exchanger stack.
If you leave the heat exchanger unflushed for more than 2-3 years the tubes start to block with salt
(at least, they do on my Volvo) and cooling
efficiency drops dramatically.
When laying up for the winter, I finish by flushing
a fresh water/antifreeze mix into the engine and leaving it for the duration. This kills off any marine
organisms lurking in the raw water system and is better IMHO than simply draining off the raw water.