If you have a code question, it's always helpful to include your actual code, rather than describe it.
One thing you should bear in mind is that the FILE attribute of <cfcontent> references a file (on your file system), not a URI. So it's inappropriate to include URI-specific elements in that value.
The fragment part of a URI (the bit after the #) is only relevant ot he browser, so to hit that fragment, it needs to be in the address the browser requested. It's nothing to do with what you send back (you just send back the document).
You coudl conceivably use <cfheader> to tell the browser to fetch the URI with the fragment, and then from that URI return the PDF file. The browser should then - if it suuprts PDF fragments - work out what to do.