This question doesn’t seem centrally related to Lion Server, save for the directory path related to the web server.
Look around under /Library/Server, (/Library/Server/Web, IIRC, but it’s been years since I’ve been running Lion Server, and the Server.app moved the directories around once or twice over the various versions) and you’ll find the web server directories buried under there.
Then check the organization of the PDF files you're interested in, and work from there.
Basically, find the files you're interested in, and either copy those, or post an example of the path(s) and file(s) for the source files for the transfer, and somebody here dan help with a bash command or shell script or similar. (I haven’t had a 10.7 server around in a very long time, unfortunately.)
It’s also possible somebody has enabled per-user directories within Apache, which means the PDF files would be under per-user directories in each user login.
If you can’t find the files, find the name of a file and use the following shell command:
sudo find / -iname foo.pdf -print
That’ll search the entire file system for all files named foo.pdf. You’ll need to enter an admin password for the sudo, as root access is needed to override access and search everywhere.