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Hi, Tom here.
The reverse polarity code simply means that you need to reverse the two 120 volt lead wires (L1 and L2 or it may be labeled N or Neutral).
I know it seems strange that they would have a reverse polarity code for ac current, but it has to do with the flame sensing circuit which operates on a tiny direct current signal. It wants to see the neutral or ground from your power supply on the correct input terminal.
Just switch the two power leads and it should go away.
If it says reverse polarity you need to reverse the power leads. The circuits on the new board could be different.
Yes, it's not going to harm anything, the worst that can happen is what it's doing now.
I would try it.