Yeah that's true and it's why everything else has to be done in pen, but I've always been told they make an exception for diagrams even in my business GCSE so it should be fine! I think the issue with the scanners is more that it picks up traces of anything you rubbed out previously but again I wouldn't worry too much as they'll still get the gist of your diagram. It doesn't say to go over them on the front of the exam book so they shouldn't really criticise! 😅