Matt Cutts a renowned Google spam team head tweeted a SEO tip on 25th march not to deleted your old disavow links file before you upload 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.
— Matt Cutts (@mattcutts) March 25, 2014
Mostly when we upload the disavow link file it override the old one. On twitter many ask for a clarification on this subject they what will happen in case of override file. Matt Cutt clarified again on twitter.
Some SEOs have been deleting the file first, then uploading new, which creates two emails, and sometimes that confuses folks. — Matt Cutts (@mattcutts) March 25, 2014
According to Matt the issue is on two emails which make a confusion. When you will delete the old file Google will send mail When you upload you will again get email. So the better option is to override the old disavow links file.