Hello Alex, I believe you are referring to my D3-110 failure. When I experienced my water ingest issue, it was after a fairly calm trip up from Florida to the Chesapeake Bay. I ran the engine quite a bit, as I recall the wind was not great, but that was now more than 4 years ago, so I cannot remember all the details of what happened.
I understand exactly what you are suggesting though, in that water could potentially enter into the anti-siphon loop if un-expelled water collected in the cockpit. But I can say for sure in my case, there was no water in the cockpit from waves. And in my situation, I am really certain that water did not get forced into the exhaust loop on a starboard tack. I have seen the flapper that Amel installed first hand, and it looked OK to me (it is really kind of a tube), so again I think my issue was that the engine was not expelling the water through the muffler. I surmise that it was "back-washing" if you will into the exhaust manifold and hence entering the cylinders in spurts - not enough to flood and lock the engine, but enough to seize the valves and kill it once it sat for a week.
Hope that helps.
Amel 54 Phantom #44