> A site 
> www.example.com/filepage/files.html 
> has a bunch of links to PDF files that we need,
> which are stored in 
> www.example.com/xyz/pdf/
> and we want to download those PDF files.  The
> files.html page also unfortunately has a link to 
> www.example.com

Use something like:
Options / Scan Rules
-* +www.example.com/xyz/pdf/*.pdf +www.example.com/filepage/*.html