Both highlighting as well as pen strokes are stored in vector format and the eraser does not distinguish between them.
There is a workaround to delete the highlighting on handwriting:
- Select the eraser and tap on it again to access the thickness options. Then tap on the gear in the upper left to bring up the eraser settings.
- Activate "Erase Entire Stroke". Now you can zoom in to the position where you want to remove the highlighting and tap on a part where there are only highlighting strokes, with no underlying pen strokes.
- Repeat for every highlighting stroke you want to remove.
This works best if you set the eraser to the smallest size.