If there is a problem with the wheel motor and wasn't caught the pump gets trashed. If the system wasn't flushed after the pump rebuild then most likely the pump has been damaged from the debris floating around in the system.
Hydrostat systems for the most part are a closed loop operation. Meaning as you change directions the oil in the pump goes to the motor and then back to the pump. the only oil that gets filtered is the oil that is lost in operation. So if a hydrostat system is 90 percent efficient that means 90 percent of the oil between the pump and the motor is being recirculated and the other 10 percent gets returned to the oil tank and is filtered as needed to replenish the oil lost from the loop, .Any debris in that closed system then get recirculated between the pump and the motor causing damage