Grade validation can only be used for Foreign Language classes and Math classes not Science classes. So getting an A second semester in your Math course validates the D for 1st semester. For Chemistry, you will only have a passing grade for 2nd semester which does not validate the D 1st semester. Also, if you do not retake the 1st semester courses, your D grades will be included in your UC GPA calculation.
Taking and passing AP Chemistry will not replace the D if the original Chemistry class was not AP Chemistry.
Since Senior grades are not considered for UC admissions, you are stuck with the D’s on your transcript which will definitely impact your UC chances.
Unfortunately your counselor gave you incorrect information in regards to your Chemistry class.
http://admission.universityofcalifornia.edu/counselors/q-and-a/validation/index.html#1