puoi creare un frameset dinamico nella popup
codice:
<script language="javascript" type="text/javascript">
function apri(indirizzo_pdf,titolo){
frmset=window.open('about:blank','_blank','width=640,height=480');
frmset.document.write('<html><head><title>'+titolo+'<\/title><\/head>')
frmset.document.write('<frameset rows="*,0" frameborder="NO" border="0" framespacing="0">') 
frmset.document.write('<frame name="pdf" src="'+indirizzo_pdf+'" scrolling="auto" noresize="noresize" />') 
frmset.document.write('<frame name="nascosto" src="about:blank" />') 
frmset.document.write('<\/frameset><\/html>')
frmset.document.close()
}
</script>
progetto.pdf
ciao