If the burner area and control circuit board were soaked, all bets are off as to how the water heater might function. I would guess the water had the control board shorted and after the area dried out, things returned to normal.
The large open tube the burner fits in is a hollow passage through which the flame and heat it generates follows from the burner to the exhaust. This pipe is inside the water tank and allows the heat generated the most surface area contact with the water inside the tank. It is open at the exhaust port and the burner.
Circuit boards that have been wet usually dry out and work ok a time or even two. The downside is that sometimes they continue to corrode and eventually fail. Might get a can of electrical part cleaner (radio shack should have it) and spray the board and connectors to displace any moisture.
Jeff & Cindy
'09 27FB Flying Cloud
'91 350 LE MH