Not sure if you have any programing experience but you could use the workgroup API to get them all pulled out of WPDM and also use the EPDM API to get them in.
No real serious programming experience. I see there is an API call for WorkGroup to save a PDF document out of the vault (SaveAsPDF), if one exists in the vault (IPDMDocument::HasPDF). I don't see anything about what the file would be named, but hopefully they would not all be named _PDF. I would want them to be named after their authoring document, just with the .PDF file extension. When a PDF is created in EPDM, is it automatically referenced or attached to its authoring document? I would want a reference created for the PDF document in EPDM to its authoring document. Seems like this is possible from what you are saying Clark. Worst case, we could manually create the reference in EDPM for each one after the PDF's are checked in. I would also want the revision of the reference PDF to match its authoring document as well.