Assuming the series wiring is in place while attempting to charge, I think the charger will diagnose reversed polarity when wired to either of the two trolling motor batteries -- guessing it won't go to a charge cycle. Think you will end up removing the series wiring between batteries before you can charge either of them.
In keeping with the Coach Wooden quote Bruce shows, I would read the charger manual and check the FAQs or helpline if any doubt. (And....post back on what works. Thanks -- curious.)