I go to a public school with 980 students in my grade. A new school counselor was hired this year to advise approximately 500 students. I only met her for the first time during my first of 2 20-minute college meetings.
Although I have a 4.5 GPA (weighted), 3.85 (unweighted), (10) APs, 10 Honors classes, and 3 college courses, my college counselor does not know me at all. I can't imagine she could possibly write me a memorable recommendation when she advised me to take college algebra instead of Calculus 1 (I am in College level Differential equations at this time). Do colleges consider that public school advisors don't always know their students, and understand not to take those letters of recommendation too seriously, since I can only assume it is very generic.
I do not believe it will harm you at all. Your counselor might have a questionnaire to get to know you better, or she might ask to meet you one-on-one to get a better feel for how you are as a student. From what I've seen of the CommonApp counselor recommendation form, it's not super comprehensive. I doubt you will have any problems in that area, especially if the rest of your application is good.
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