I recently did this to three of my stories as I'd re-submitted them edited together as one and wanted to avoid duplicates. Laurel would very much like to know the reason for deleting the story, but she was very clear that it was all up to you. The story and reasons are your own, do with them as you will.
If you are deleting multiple stories, simply name the story 'DELETE' and list the stories in the body-field, adding any reasons (if you want to) in the comment field below. Took 4-5 days but was no issue.