The potable side of a water heater is basically just an insulated tank. The inlet side has a tube that directs the incomming cold water to the bottom of the tank where the heater elements are, and the outlet side picks up water from the top of the tank.
If you remove the check valve from the inlet, you should be able to run water through the tank from either direction as well as in or out the drain. There isn't a place to clog, and since the water is probably already filtered by a screen on the pump and you're using clean water to begin with, there should be nothing in the system to clog it anyway.
There's an anode in the tank but if it broke, the pieces would sink to the bottom. They would not block the flow.