The waterbox will have some amount of freshwater in it normally, it should not be full of or filled with water as a maintenance procedure, though. While engine is running with hull in water, water is injected in various locations of the exhaust system and mixed with the exhaust gasses to maintain reasonable exhaust system temperatures.
Leaving a hose connected to the cooling system reverse flush port out of water on the trailer while the engine isn't running will flood the exhaust system with water, not good when water from the water-flooded exhaust system backs up through the exhaust manifold and floods the engine cylinders with water.