1. Open the PDF document in Highlights
From the menu bar choose File > Open. Locate and select the file you want to open, then click Open:
The PDF opens in a document window:
2. Click the highlighted text you want to remove
This will bring up the annotation popover:
3. Click the trash button in the popover
The highlight is removed from the PDF and the highlighted text and any attached comment no longer appears in your notes.
If you instead want to highlight a different part of the text you can follow this guide.