Separate charge and discharge wires on your ebike battery means an internal BMS (Battery Management System). If you charge through the discharge wires, the BMS wont switch off the charger. It also might not charge at all if there is a low voltage FET cutoff.
If it does charge through the discharge wires, it may not properly balance the cells and one cell will always get overcharged. You would need to charge with a timer which switches off before any cell hits the HVC (High Voltage Cutoff).
I would charge through the charge port, it's there for a reason!