> think not) just some missing files (pdf's) that I
> was able to manually download and place into the
> folder HTTrack had indicated.

The files might be there, but the HTML pages still point to the online version
(there is no magic: the HTML files created by httrack are static files, and
links have been rewritten to point to the http:// external form)

You may consider adjusting the scan rules (Options / Scan Rules) by adding
something like "+*.pdf", and re-running HTTrack using "continue an interrupted
mirror" (not "update", too slow) to get these files and rewrite the links
properly.