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I have had a similar issue and we had to remove PDFs in order to clear a penalty. Having said that, the PDFs that were linking to our site were very spammy and purely written for SEO with unnatural anchor text links (So Google rightly penalised them). If the PDF/s of your client (it would help if you told us which one it was) were very high quality and not written in the standard spammy SEO way then I don't think that you have as much to worry about. Finally, all the sites you have listed are PR0 and of very poor quality removing them is unlikely to have a negative impact on the site that you are optimising. Hope this helps.

Thanks Keri, I'll give this a try and see what I find.