If cache is the issue couldnt you use something like a php header to stop the browser from cacheing? I am not certain if it would work, but I think it should.
// Date in the past
header("Expires: Mon, 26 Jul 1997 05:00:00 GMT");
or force them to download the new .pdf file with something like
// It will be called downloaded.pdf
// The PDF source is in original.pdf
Again I am not certain if this will work, someone else might be able to confirm or refute this.