It shouldn't hurt. The new smart chargers will charge each battery individually.
Marine batteries and AGM batteries can take a lot more charging cycles than
the normal starting batteries. They are made for that due to running them down
to hardly nothing with the trolling motors. I wouldn't worry about it. Leaving it
discharged will do more harm than good.
Correct charging can knock off sulfate build up on the battery plates, if you have
the correct charger. That itself will help keep your batteries in good shape.
If you have a book on your charger, read it. It will tell you a lot more than you
will ever need to know about batteries.
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