Levi, I understand what you are saying and indeed you raise some interesting points of discussion. See this שקלא וטריא in which these questions are analyzed at length. למעשה, if the ger was frum if even for a brief period of time we say דברים שבלב אינן דברים and given that בית דין saw no sibah or siman to make us think the ger wasn’t mekabel we assume everything was kosher after we see he was frum initially. The Rambam writes that he has the din of a Yisrael mumar. (I only saw these just when I went over this )
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