Batteries reversing polarity
Plus most trolling motors have some type of circuit board in them today. If you leave the circuit connected and if you get a voltage spike you can fry you circuit board in your trolling motor.
So either unplug the trolling motor or what I did is installed a master shutoff switch on the jumper between the - & + terminal. I opted for the switch because continuously unplugging a plug can wear them out.
Have a good day.
When charging you should have the two bank charge with leads on each battery, but have a switch or unbolt the wiring before you plug in your charger so the you treat each battery as a separate unit and it can't backfeeding to the other one and possibly causing reversing polarity.