Yesterday, Matt Cutts, Google's head spam fighter, posted on Twitter that you should not delete your old disavow file prior to uploading the new one.
He said on Twitter:
Quick SEO tip: no need to delete your old disavow links file before uploading a new one. You can just upload the new one.
Why? He clarified shortly after on Twitter:
Some SEOs have been deleting the file first, then uploading new, which creates two emails, and sometimes that confuses folks.
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?
Quick SEO tip: no need to delete your old disavow links file before uploading a new one. You can just upload the new one.— Matt Cutts (@mattcutts) March 25, 2014
Forum discussion at Twitter.