The author cannot make any changes to a paper once it has been submitted. If you have not already sent the paper out for review, or if no reviewer has uploaded a review for it, you can use the new paper if you want. As always, blind it, add line numbers, and convert it to PDF. Then delete the existing PDF and upload the new PDF. Do this on the paper’s Desk Review tab by deleting the old PDF by clicking the x, uploading the new paper, and then clicking Save. See What to do if you upload the wrong PDF.

If reviewing has already started with one or more reviewers downloading it, you can email all the reviewers for the paper to hold off reviewing and ask the Managing Editor to delete the existing PDF so you can upload its replacement.