You will need to take a more scientific approach to figuring out why one of the batteries is failing.
When wiring batteries in series, your batteries need to be matched. Same capacity.. which generally means using cells from the same manufacturer and age. Of course one would expect the older cell to degrade and fail each time, but it seems from your description that perhaps it is always one cell that survives.
Be careful not to mix capacities of batteries. Batteries have a cold cranking amp rating, but also a continuous discharge rating. I would suspect that the continuous discharge rating is more pertinent to this kind of problem.
When the system is drawing current, the same amount of current is being passed through all the cells. (Each 12V battery has 6 cells). If any cells are weak, then they will appear resistive and actually develop a voltage in the reverse direction. If you monitor the voltage on the battery as you run your trolling motor, you may see the voltage drop off on the weaker battery at a faster rate than the strong battery.
Were I going to figure this out, I would choose to wire in two voltmeters, one across each 12V battery, and then monitor the discharge of each battery on the next outing. What you are looking for is for one battery to drop to around 10V or lower with a load applied, while the other maintains a 12V charge.
If you run batteries for a period of time with one of the cells is weak and becomes reversed, it ruins the cell… essentially, it becomes charged in the reverse direction which causes the two plates to become similar in composition and no longer functions as a galvanic pile.
The other point made in a post by another member was to check the charge rate. Measure the voltage across the cells during charging. Check to see that both your batteries are getting the same voltage (around 13.8V like your car’s voltage regulator). If one of your chargers is outputting above 14V, then it can overcharge that battery and shorten the useful life.
Personally, I would suspect that your charger might be overcharging the cell and boiling off water causing the same battery to be observed to fail repeatedly.