I assume that the engine is a 16hp Kohler as the only tractor you have listed is that grand old Wheel Horse.
If it were me, I would pull that engine and tear it down now, before something bad happens. Those engines are indestructible if properly cared for. That being said, everything wears and in different places, according to the manner in which we use them. Might be a rod bearing, piston slap, worn rings, wrist pin, or maybe the valves. In any event, it will need to be fixed. Even if it is a valve, to properly fix it will necessitate pulling the engine and tearing it down.
Do it now and you may only have a small problem to fix. Wait and keep running to diagnose the problem may cause complete failure of a vital part and further damage the engine.
Nick