This is a good question!
Please tell me about the 12V to 36V DC to DC charger you have as that set up is alluring to me as well.
Okay, charging, charging only occurs due to potential difference in voltage, in other words the charging source voltage has to be higher than the battery being charged to get the electrons to flow that direction, or there is more electrons on the charging side than the being charged side. Make sense?
In your current configuration, when you have the engines running, does the dvsr close and try to charge the house battery while the start battery is being charged and charging the trolling motor battery? If so, what is the connext battery voltage reading?
Since the resting voltage of a LFP house or start battery is 13.6 volts when it is fully charged, that will activate the dvsr since its close point is 13.4 volts, (opens at 12.7 which is when a LFP battery is almost fully depleted) when that happens, the proposed LFP house battery could very well start “charging“ the trolling motor battery bank until such time that A-the LFP house battery voltage drops enough due to charging the trolling motor battery-that whole potential difference thing, or B-IF the alternators are supplying high enough voltage to keep the electron flow INTO the house battery at some level with the dvsr closed.
The alternators on our boats only produce roughly 13 amps each, maybe 14, but the point is, there is not a lot of left over charging power, their full output is at 3500 rpm’s, the most I have ever seen on my boat was 26 amps flowing into my LFP house battery but dropped off relatively quickly as the battery voltage climbed as the battery was being charged. That being said, the rectifier / regulators which convert the three phase AC voltage from out alternators to DC and then regulate the voltage to 14.4 volts by shunting the excess voltage to ground when it is unneeded will charge aggressively with the addition of a lot of load which drops the voltage. Don’t worry you will not over burden the alternators, the alternators in our boats are always at full output since their magnetic fields are fixed, they are known as PMA’s or permanent magnet alternators which are different from automotive style alternators which regulate the output by altering the current flow into the rotor or magnetic field on the rotor, these types of alternators can be easily damaged by LFP batteries unless there are protections there, either thermal within the alternator or just current limiting.
In my opinion, you need to set your dvsr activation up on a rocker switch on the dash so that you can control when it closes. Also, you need to put in a couple of victron smart shunts so you can monitor the amperage flow into or out of the trolling motor battery bank on the load side of the DC to DC charger, and another one on the house battery so you KNOW what is going on
That DC to DC charger is going to be looking for enough voltage to operate, and it should have a charge relay, dvsr / ACR itself so that once the proper input voltage is present it will close and begin charging, voltage too low and it will not operate. That is why I asked above whether or not the dvsr is currently operating and what the connext screen voltages are. To be clear, there should be no flow from the trolling battery bank back through the DC to DC charger due to the step up transformers and diodes, as well as its internal acr.
Should you disconnect the dvsr ? NO.
But you will need to have more control over it on the dash so that once voltages look good you can activate it and let the engines charge the house battery too. Simply hooking the dvsr up to a run hot will not work in your case as you need to make sure the power flows are correct so that you are not draining your house battery to charge the trolling motor battery bank via the DC to DC charger.
Does all that make sense?