Yesterday, Matt Cutts said, Google’s head spam fighter, posted on Twitter that you should not delete your old disavow file prior to uploading the new one.
“Quick SEO tip: no need to delete your old disavow links file before uploading a new one. You can just upload the new one.”
I am not sure exactly who it confuses? Probably the folks at Google who review disavow files for manual actions.
So I guess, just upload the new one that will replace the old file?