You don't need to manually upload PDF files and then link them. WordPress has a built-in Media Library you can use that will be preserved through updates. And I'm 99.9% sure that stuff you manually upload won't get overwritten. Especially if you upload them to a custom directory such as /ebooks.
Back to the Media Library function, when editing a page or post, there's a Media Upload section right above the text editor. The last icon looks like a multi-pointed star called "Multi-Media," or something like that. I use it to upload PDFs to my site. It'll create a link in your page/post using the Title you assign to that upload as the link text. It will also become part of your Media Library which you can browse from the left-column link in wp-admin.