Tool to compare large numbers of PDF files?
There is quite a few software products that claim to diff pdfs. I've never had need to use one but if this is going to be a recurring process I think it'd be wise for your company to invest in one of them. Just Google "pdf diff" for a bunch of potential applications.
Additionally, your situation is very similar to this question: http://stackoverflow.com/questions/145657/how-to-compare-two-pdf-files I think its discussion may help.