I'm going to try to suggest to possibilities and ask some questions in blue within your post for clarity.
This problem has occured 4 or 5 times in the last season. The boat is left in the water for the season. The cockpit is constantly covered and so are the filler caps.
The boat, motor gas tank and lines can still heat up and cool down despite being covered. No marine system in a common recreational boat has a sealed fuel system like modern car. Air and moisture can enter your tanks, carburetors, and fuel lines though the tank vents, carburetor jets, and the interior carburetor passages and mix with the gas in the tanks and lines despite the boat cover and anti-siphon valves.
The carbs were rebuilt by a highly regarded shop after it happened the first time. It happens in both warm and cold weather.
There's still temperature changes under the boat cover, rain, shine, or both.
I get fuel from several sources and mostly marinas. Shortly after starting the 2 Honda 40's one of them quits. It will not restart.
Is it always the same engine?
I disconnect the fuel line and bleed off a pint or two of liquid that looks like cloudy lemonade.
Probably has water in it as microscopic droplets.
I re-connect the fuel line and restart the motor with lots of choking, killing and short running before it works its way out and runs fine for several trips.
The interval between these trips is probably short enough to minimize the moisture absorption in between.
Fill caps and vents are tight and waterproof.
See above.
The cloudy lemonade like liquid turns back to a crystal clear orange gasoline after sitting for awhile.
Heat probably drives the water droplets out.
Everything runs great for a few weeks and then strikes again.
Has the interval between these trips been longer or the weather more temperature varied?
I always fill both tanks at the same place and time with the same amounts. I have used isopropyl alcohol on two occasions.
100% isoprophyl alcohol will absorb moisture, help stabilize/stop the gas breakdown, and help water pass it through the system, but your gas mix is probably already 10% ethyl alcohol from the pump, + any other absorbed..
I know about condensation but this is the first time in 5 years this has happened under identical storage conditions.
Has your gas mixture, formula, or alcohol % changed this year?
The one thing that has changed this year is I raise the motors after use now.
This may affect the ability of expanding/contracting air to draw moisture through the carburetors, fuel filters, and lines. Do you have fuel filters on the motors themselves? Are there Racor or other filters in the fuel lines between the tanks and motors? Do you drain and change them regularly?
Any similar cases or solutions?