Short answer = Yes, you should not damage the onboard converter.
Some smart chargers (Xantrex as an example) will start a three stage charge cycle with constant current, you may get 55 amps until the battery bank reaches 14.5 volts. This will charge the batteries so much faster than a regular charger at 13.XV. Once the batteries reach 14.5V the charger will switch to constant voltage and hold the output at 14.5V until the amperage being delivered falls below a threshold, like 10A, at that point the charger goes into float mode and effectively shuts off allowing the battery to drift down from 14.5V to the float voltage of 13.6V at which point the charger will produce power on demand to keep the battery bank from falling below this point. None of this should interfere with the old/dumb charger on board, you should be able to fast charge your batteries from the genny.
That being said... why don't you just install the three stage charger in place of the old converter?