The lead batts probably needed DC-DC staged charging more than the lithium does. Lithium does fine with "charge and stop".
The
stop part is problematic with actual isolators (diode or FET-based); due to how they are wired in there is no easy way to stop them. If the isolator is a relay/combiner/solenoid it can be
disabled at will.
But depending on DoD, how long you drive, whether the isolator is diode- or FET-based or a relay, and the voltage of the alternator you may not get to the
stop part anyhow.
The DC-DC isn't designed to protect the system from load dump. It provides setpoint-based charging and current limitation. The starter battery would attenuate any dumps.
But the play is at first base: prevent load dump by not overcharging and tripping the BMS. Most default Li profiles are too aggressive, IMO, and can actually
cause BMS disconnects.
Fullriver AGM? If so, I'm guessing the bank pulled something like 75A through the isolator at 50% DoD. And, based on other charging reports, that the 300Ah Li bank would pull ~100A. Not a giant jump there, assuming the components are happy with that.
Before yanking everything and buying new parts you might try it with the isolator in place.
An actual isolator would need to come out to install DC-DC, since an isolator sits between the alt and battery and lowers voltage (forward voltage drop through the diodes). A relay could remain in place if you wanted.