Believe this is most likely a result of the PDF file not being available on the QVS side, would ensure the file is populating to either of the following places:
QlikView Management Console (QMC)\System\Setup\QlikView Server resource\Folders tab\Alternate Temporary Files... location
The files should be appearing in one of those two locations and need to be sure they are still there when the user attempts to actually download the file. There is a Settings.ini setting that may be in play too:
Server Temp file timeout
About all of which I can think other than anti-virus etc. or something in IIS messing with things if you are using IIS instead of the QlikView Web Server. May want to consider using client web browser Dev Tools to trace things or Fiddler to try to see what is going on in further detail that way.
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