Use VIPRiser to "print" a new PDF. Note you can batch print a number of PDFs all at once from the Finder. They can be saved in a folder (see vipriser preferences).
VipRiser changes the names (adds characters before and after the .pdf). Use NameChanger to remove the leading characters and the extra .pdf on the end. Again, you can do this to a large number of files at once.
So basically print to VipRiser which will create new PDF files.
Then rename the PDF files back to their original names.