Lots of our clients have the issue of broken links in ancient PDFs and changing/deleting content is not always a permitted or desirable option for them. 

However, several of our users are updating the PDFs by removing the hyperlink and leaving the URL as text - some will add a note saying the page no longer exists. 

This maintains the integrity of the original document but ensures that people don't click on a useless link that no longer works, which is an irritation we should seek to avoid.

Having the original source of PDFs can also be a problem.  However this has been resolved in the latest version of Adobe Acrobat (version 9) with the addition of the Export feature allowing you to export an existing PDF to, say, Word (retaining all formatting) so that you can edit the document and then convert it back to a PDF.  Take a look at a demo here http://www.adobe.com/designcenter/video_workshop/?id=vid0333&trackingid=EWLWW

This feature could also be used if tagging an old PDF for accessibility has proved problematical in the past.

I believe this approach would address concerns of removing errors from a Sitemorse audit without compromising the integrity of the original document.

If, however, making any sort of change to the actual documents is impossible / impractical / banned then an alternative may be to consider creating an area (perhaps as even a sub site / subdomain etc) that we don't review, you could then put all the 'old' pdf's that you can not change or alter in this area, make it clear that that area has old documents that may offer limited capability.

It's not Sitemorse's intention to encourage people to take inappropriate actions (to delete an old PDF that should remain on the website) in order to maintain their positions in the Surveys we run.  The audits we run and the information they contain are an invaluable source of information for organisations to maintain the highest possible level of site quality and user experience possible.