If you don’t pass the required CSU courses, Cal Poly will likely rescind admission.
To my understandng, Cal Poly uses the CSU GPA which only includes eligible courses for 9th-11th grade.
http://admissions.calpoly.edu/applicants/freshman/criteria.html
http://admissions.calpoly.edu/applicants/appchanges.html
As for Purdue, don’t they have rolling admissions? This means they may process and release your decision before you have a chance to update them will fall grades. I’m not as familiar with Purdue though, so someone else might have a more concrete answer than I do.
I was mainly generalizing and talking about private schools in my post. If you have questions about specific schools that can’t be answered through their admissions website, it’s best to just email or call their admissions office.