Hum! I'm not with you. You say on one hand "each page is an individual QXP file" and on the other hand "Is there a plugin or script I can use to automate converting all the pages to individual QXP files"... Can you tell us more precisely what you have and what you want? It would be helpful to us to helping you :-)
Oops! sorry I see your answer in the thread title: you have multiple QXP files in as many folders and you'd like to PDF each file on its own, right?
An AppleScript could do that, but that's not that simple. To put it in some words, the script would cycle through the parent folder (containing all the sub-folders containing each one a QXP file and all the stuff along). Then it would PDF the file, provided everything is OK with each file, with all the links, all the fonts, etc. A good script would have to check everything in order to output correct PDF files. Of course if you are sure all the QXP files are OK and that you don't fear any alert message, things would be a bit easier but one never knows.
Have you searched the archives? I'm pretty sure the subject already turned up a while back.