A rule of thumb for using circuit protection with batteries is that the primary circuit breaker or fuse should be within 18" of the batteries. That rule is sometimes stretched to accomodate RV construction details. I have one bank of 6V batteries and the primary 150 A breaker is attached to one of the battery's positive terminals, the same terminal that leads the (+) wire to the distribution panel.
A user of 6V batteries and circuit breakers can weatherproof the circuit breaker by covering the breaker and terminations with a material that is waterproof like silicone, Dicor sealant, Plastidip, etc.
You haven't posted any voltage measurements of the charge current, either during charge or when in use, now that the batteries have been recovered. I would hope that you use even a cheap hand-held meter to suss out what is actually happening with charge current to the batteries. I'd also suggest to buy a glass tube battery hydrometer to measure the specific gravity of the battery cells. That is the final arbiter of battery health and will eliminate worry, speculation, or the inevitable tail-chasing that is typical when dealing with compromised RV batteries.
FWIW, at one time I was responsible for the upkeep and maintenance of a fleet of 300 6V batteries (golf course fleet). My learning curve was short and steep. It became apparent, quickly, that 6V batteries like higher charge voltages (14.8V and higher) when being charged and that float charge introduced immediately after use promoted battery longevity.
It seems you've developed a plan to insure charging, even in bad weather by relocating the circuit breaker. I think the cold weather, when you tried to use the batteries on your trip, may have been the defining factor. Using a 700W microwave and an inverter would draw approx. 60A-70A through the circuit breaker and cable. In most cases that is enough heat in the cable to melt any ice or snow on the cable. A 40A charger would return the same results.
Good luck with your 6V batteries. They are a good solution for most RV power siuations and are very durable. If you were to add solar charging, you could be assured that your batteries would be charged to 100%, eventually.