If you can move the “rod” up and down then your TRD (Thermal Release Devise) is broken. Most likely you will find small grains of glass the size of sand in the bottom. This most likely broke when the air passage way, 1″ from the bottom, became blocked by your flooded conditions causing the burner chamber to over heat and tripping the TRD. I’m afraid warranty doesn’t cover this kind of flooding and your heater will have to be replaced. Some home owner policies will cover flooding.