Will it cancel out?

I took algebra 1 and geometry in middle school. My semester grades for algebra 1 were B,A. For geometry, I had B,B. These letter grades show up in my transcript in the middle school section, but hey are not counted in my HS gpa. I got 800 SAT math section and 800 SAT math 2, and A’s in all math classes after that, including multivariable calculus. Will my middle school grades be overlooked in admissions?

Yes, those middle-school grades will be overlooked. Except in rare situations, middle school grades NEVER matter in the college admission process. Certain classes taken in middle school (typically math and foreign language) are counted for credit and towards the number of years that a student has studied that subject. But the grades themselves are NOT considered.

Colleges will view you as a very strong math student and—if you should go on to a math-related career—you may one day chuckle about those long-ago B’s!