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Sounds like a good excuse to get some new bonnet stripes !
You could touch it up but it won't match very well. Not only would the color be just a bit off, the finish wouldn't quite look right either and it would stand out like a sore thumb (especially to those of us whom are OCD).
Stripes are inexpensive and easy to put on. Of course, taking the old ones off can be a bear, depending on several factors (how long they've been on, has the car been garaged, how were they installed, OEM or aftermarket, etc).
+1, as long as it's not all the way through the vinyl to the paint, I'd use a sharpie to touch it up for now. If it IS all the way through, then just replace it. You should be able to get one stripe from wherever they came from (either the dealer, or whatever vendor made them for you) OR it's a good excuse to get something new and custom!
) I'd remove them, clay, polish, and wax the bonnet. 
