It would be good to obtain a schematic for that control board to understand what the 3A diode does. Few people who manufacture and seek a profit place components on a board that are unnecessary. If your motor is more powerful you may need a "more powerful" diode to do the job of the SM3 that may just have been destroyed by the more powerful motor.
Seen from the point of view of trying to be logical. If I have a 100mA fuse and 1Amp circuit, and the 100mA fuse keeps blowing, do you think I should use a smaller fuse or no fuse at all to solve the problem?
Perhaps more fruitful to compare the board capability to the motor, rather than the motor power to what you want the board to be able to do. Facts make circuits work, not speculating without consulting real capability.
Try to get hold of the control board specs/user manual, and the schematic if that's in any way possible (maybe not), that will help to decide if a larger diode will solve the problem, or if you may need to re-think using the motor and control board together, and may want to look for a workaround solution to find compatibility.