If it really is as much as 6" low at 50', you are going to have to remove a lot of sight to zero. Unless the sight is quite tall to begin with, you may have to remove enough that you'll see the top of the slide in the notch. I had to correct a .45 revolver that shot a foot low at 25yds, and luckily the front sight was about 3/8" tall, so I could remove a lot of it without messing-up the sight picture.
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