Bypassing Charge port on brushed controllers with SLA's Batteries

By passing none working charge ports on brushed dc controllers. I've got a 36v SLA powered 800W Kids Dirt bike and a similar 36v SLA powered DTX Razor Drift Trike. Both controllers appear to have duff charge ports and when the chargers are plugged in the LED remains green and wont charge the depleted batteries. However if I disconnect the batters from the controller and connect the drained batteries to the charger direct the green led turns red and they start to charge. After the voltage gets to 42v the chargers switch off and the red LED turns green.
I'm I ok bypassing both these vehicles controllers charge port connectors and wiring the onboard charge ports directly onto the SLA battery's. Would I have to wire a battery isolator switch or charger switch over to disconnect the power lines to the controllers before charging in this way.
How do the charge ports work on these controllers is there a component internal fuse etc I can replace to get the charge ports working again as before. Thankyou.