Concern in philosophical inquiry

I heard your argument that there is not much to fear from philosophical inquiry, since it merely reveals whether I already believe, so that if it reveals that I am an unbeliever, it is essentially a retroactive discovery, and if so, why fear it?
 
Indeed, a convincing argument. But I fear that it was prepared against the intellectual investigation because, perhaps, the person will become confused during the investigation, meaning that he actually believes, but because of their logical arguments, then he accepts the belief. But this is not a retroactive discovery, but a product of confusion.
 
I asked: How do you deal with the argument of this concern? And do you have a way to minimize the concern?