The odometer reading reflects the vehicle's total mileage, not the engine's mileage. While you can record the engine's mileage separately for your own records (it's a good idea to do so for maintenance purposes), you cannot legally alter the vehicle's odometer reading. Any attempt to do so will likely damage the vehicle's electronic systems and invalidate any warranty.
Instead of attempting to reset the odometer, simply maintain a separate record of the engine's mileage. This record should be kept alongside any maintenance records related to the new engine.