Something doesn't smell right here. Lol!
You may first want to try and better determine the failure mode for those batteries. Did they indeed short out or were they heavily discharged due to a load applied to the battery bank?
There's a difference.
If this was an OEM installed autopilot, I'd find it hard to believe that they didn't have adequate circuit protection in place to prevent a dead short going all the way back to the batteries (regardless of age). You didn't mention it but if this is indeed a Hatteras, they're some of the best engineered boats in the world so highly unlikely they'd lack appropriate breakers, fuses and/or thermal overloads to protect the main 32 volt system.
I'd suggest the following:
1. Disconnect all the batteries in the affected battery bank.
2. Measure voltage across the terminals on each battery. If you get a voltage reading other than zero then it's not likely a dead short in the battery.
3. If you do get a voltage reading, I'd take the batteries to a auto/truck battery store or wherever you bought them from and see if they can bring them back to full charge. As others have suggested, this would take specialized equipment.
4. ALTERNATIVELY you could try and bring them back to full charge yourself, but that would require a good 8 volt battery and an eight volt charger. Wouldn't suggest this step if you don't know what your doing because bad things could happen otherwise.
All that said, the batteries still may be toast, however since they're new, I'd at least make some further attempt at determining condition and possible restoration rather than just chucking them.
My 2 cents.
