Thanks to @BrianFegter comment, I was able to find and fix the problem. It was just a problem of case-sensitivity. My development environment, http://serverpress.com/products/desktopserver/ , doesn’t have a problem with finding the pdf when the file name was caps and the anchor tag link was in lower case. My hosting provider seems to be the problem though, so I just changed all files to lower case and that fixed the problem.
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