Dear Wattpad Woman…
Leave the short story up while submitting your novel, at least, as proof of its medal status. Your future agent or editor may prefer you take it down when the novel goes into production because you’ve revised the story so much, but not necessarily. In pre-Internet days, published short stories that grew into full-length novels had no option to delete the original short story from existence. The two just existed simultaneously. That precedent prepared readers to understand and accept that there are differences between a novel and the short story that inspired it. Since you’re comfortable being on Wattpad in the first place and you’re confident in your short story despite the changes you’ve made for the novel, let your medal-winning story lead readers to your new novel.