I always leave the flow going through mine, that way if the temperature drops it will automatically maintain the desired temperature. That aside, I would think it better to leave it with flow rather than by-pass it unless you plan to totally drain and rinse it. If you just valve it out you will leave chlorinated water in it and as the temperature changes you may end up with a higher potential to corrode the exchanger than with a steady flow. I have operated mine for over 8 years this way with no problems.