The heater's internal piping restricts water flow and makes the pump work harder to push water through the system. The main purpose of the bypass valve is to remove this restriction while the heater isn't being used, in order to improve water circulation and save energy.
The downside of the valve is that if it completely bypasses the heater, water will be trapped inside, and that stagnant water can damage the heater. Which I presume is the reason you're considering draining the water.
If you adjust the valve so it doesn't completely bypass the heater, but instead directs ALMOST all water around the heater while allowing a small amount to continue to flow through the heater, you'll get essentially all of the water-circulation / energy-saving benefits of the complete bypass, but without the risk of trapping potentially damaging water inside.