1. Open the PDF document in Highlights
Tap the PDF you want to open in the Highlights document browser:
The PDF opens full screen:
2. Tap on the highlighted text you want to remove
This will bring up the annotation popover:
3. Tap the trash button in the annotation 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.