The Replace PDF tab replaces the original PDF to download.  

It will only replace the PDF when the user clicks on the Download PDF icon in the toolbar at the top of the edition (see the red outlined icon in the image below):

Replacing the PDF for download does not replace the digital edition.

The purpose of the Replace PDF for download is that sometimes, you will not want the pdf you used to create the edition be the one you want your users to download so you can replace this pdf.  That way, your users can use this pdf and you can utilize the digital edition at large.