The butt SN is the main SN. That's intact. The question remains about why the number in the yoke cut was obscured. I can't think of a reason except that it was believed too be stolen. You could ask the Police to run it. They just need the number, not the actual gun. But it's bothers you this much, I think I'd just return it.
I think you've learned a lesson here. In the future, you'll not buy a gun with similar signs of tampering.

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NRA LIFE
Reserve Officer 9yrs