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After I reread the will transcription, I also thought the reference was strange. If the John Benwell Harger was the son of his daughter, his last name should be something else. Perhaps the daughter was not married? Or perhaps there should be a punctuation after the word son? It is confusing. Also John Harger would have been 47 when John Burl Harger was born, certainly not impossible, but a bit old. I also considered that John Burl was a grandson? But, based on the family stories, it is probable that John Burl and John Benwell are not the same, I would think that the father would not feel compelled to leave anything to his astrainged son.
I will need to find a copy of the original will because I agree with you that something seems to be missing.