If you want to update or edit a file that you have already uploaded, you mustn't delete the old one and uploaded the new.
You just need to open the issue's details and select the tab "File versions".
Then, click on the "cloud icon" on the right:
If you have added any multimedia files (video, galleries, etc) and you want to keep them in the new issue, you need to activate the option "Keep metadata edits". Please note: in order to keep the multimedia links, both issues must have the same number of pages.
You can now upload the new file.