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 annotation you want to remove
This will bring up the annotation popover:
3. Tap the trash button in the annotation popover
The annotation is removed from the PDF and the text associated with it no longer appears in your notes.
If you want to add a different annotation instead, check out this guide.