When you "resurface" there's a couple of ways this can be done by nearly any auto machine shop.
The first is a simple scuff where the flywheel is chucked up and a circular stone is pushed against the face while rotating to give it that factory fresh flat surface. This removes an unmeasurable (at the auto shop level anyway) amount of material.
They can surface the flywheel which uses a cutter to remove material and thins the flywheel by whatever amount of material need to remove defects up to the max dimension of the manufacturer.
They can resurface and lighten, not that I would think you want a tractor flywheel lightened, but it can be done. They remove material form the backside of the flywheel to remove mass intentionally and then they rebalance it.
In the second two cases the flywheel should be rebalanced. I don't know if the motor is internal or externally balanced, but they need to know so they can keep the weight distribution correct for your engine.
If you wanted to get real OCD about it, you could pull the crank and pistons and have them balance the entire rotating assembly. Again, possible, but not sure of the value in tractor. Its not like they spin to super high RPMs.