After the PDF is attached to the product the option to change it will appear on product edit/add screen.
To change the attached PDF file please go to Products and find the product for which you want to change a PDF file. On the product edit/add screen find the attributes box where the PDF is attached.
Click on Choose File in Replace section. This will allow you to choose a new PDF to upload. Save the product when the file is chosen. This will ovverride the file on the server with a new one.