What exactly does the UC application say? Does it show the course as AP, or NH, in the “Hnrs” column?
Only one honors level will show up in the UC application. It won’t show both AP and HL in that column. For an AP course, it would just show AP even if your high school transcript shows “AP(HP)” and all AP courses would already be calculated into your GPA with the UC Honors weighting.
For example, this is how AP Chemistry would show up in the UC app.