Just posting my recent (long winded scenario).
Experienced an overheat alarm on my port engine just the other day (Fri 7/9). Was approaching the ramp dock in a breezy north wind and wound up having to back away to readjust the approach.. Heard a clunk when I reversed with medium throttle and within a min or so got the overheat on port and found no water coming out of that pisser/bypass. Shut down the engine (within 30s) after securing to the dock. Retrieved and pulled back a mile to the marina. Found the culprit to be a piece of 2x4 lodged in the impeller.
Cleared both tunnels and hooked up the hose to the port engine and ran it for a min or so and the overheat warning cleared, but the check engine remained. Shut down and ran the stbd engine on the hose with no issue. Turned key off. Waited a few mins while inspecting impellers. Turned key on and ran port on the hose again for a min or so. No further overheat and check engine remained on. Shut down and turned key off.
At this point, two starts and shutdowns for the port engine after clearing the blockage. Batteries were left on.
Covered up and drove home to check the forum to find this thread and the engine codes thread.
Realized I had left the batts on, and returned to the marina about an hour later to try what I found here.
Turned batts off for about a min.
Connected hose to port flush fitting.
Turned on batts and turned on key. Started port engine.
Check engine warning was still there, but by the time I turned on the water (~5s after starting engine), and turned back to the console, the check engine warning had cleared!
Shut off water and then the engine. Shut off key and battery. Turned all back on and no more warning light. Ran engine on hose for a couple mins and no issues.
So for me it seemed to be 3 cycles, and I only turned off the batteries for a couple minutes before the third cycle, after which the check engine code cleared. 2019 242 LSE with v39 Connext (engine hours sync fix).
Ran out on the water the following day (Sat 7/10) and water flow was normal with no further issues.
As always, great info on the site that saved the day for a beautiful Saturday on the water!
The culprit - 2x4 chunk
Pic showing port engine with warning and check engine codes set. After those cleared, the values returned to 0xC0 and 0b00 respectively.