I'll admit, I know nothing about scooters, but if the series connections are somewhere in the internal wiring, I would guess that maybe some circuits use 12 volts and some use 24 volts. I would
NOT try to charge the batteries with a 24 volt charger without knowing exactly how things are connected. The whole thing could go up in smoke. I would suggest that if you have to use a 24 V charger, disconnect them from the scooter, jumper them in series and charge them. A big PITA, but safer.
Just my 2 cents worth. (As we no longer have pennies in Canada, make it my nickles worth)