Do you want to extract content from existing SWF files? This would require a PHP library that could parse the SWF format for media that you might want in the PDF.

I'm not aware of any implementation in PHP.

For the swf format see: http://www.adobe.com/devnet/swf/

If you are able to install programs on your server, you could probably get an "SWF decompiler" to decompile the swf into source. You can then parse that "easier".

Either of the above would require quite I bit of development.

It would be easier to design the pages in a way that there is alternative content for each Flash file. So the alternative content automatically goes into the PDF. Just like how it is done for SEO purposes:

By injecting the flash with JavaScript into existing HTML node: http://www.hochmanconsultants.com/articles/seo-friendly-flash.shtml

By using XSLT to transform an existing XML file to flash version: http://www.metah.ch/blog/2008/04/holy-grail-seo-model-for-flash-and-flex-content/