Maybe the bypass valve got turned? My truck camper has three valves relating to the hot water heater. One stops water going to the hot water heater. One stops water coming from the hot water heater. The third one allow the water to "bypass" the hot water heater. They do this so that you can winterize the camper without rv antifreeze getting in the hot water tank.
Another option would be to put a battery isolator in your boat: https://en.wikipedia.org/wiki/Battery_isolator
When your cranking battery is fully charged by the motor's alternator, it will automatically start dumping extra current into your trolling motor battery.
Using the trolling motor won't drain the cranking battery with the isolator between them.