An SEO asked on Twitter if listing the same URL in the disavow link file will hurt or what happens? Does listing it twice negate it? Does listing it twice show more importance? Or does Google ignore duplicate listings?
Google's John Mueller responded on Twitter saying "duplicates don't cause problems."
John did add that it might make it hard for you to maintain the file. If you ever removed the URL, you might not notice the URL is still listed further down the list. But other than that, there are no issues listing the same URL twice in your disavow file.
In addition, if a link is actually removed, keeping the link in your disavow file doesn't matter either.
Forum discussion at Twitter.