I recently provided a method for dealing with PDFs rejected by the CM/ECF filing system (as it is implemented by the U.S. District Court for the Central District of California). That method is detailed here. While that process of exporting a problematic document out to a new document format (XPS) and then back into PDF deals with a number of problems, not everyone will find it to be a comfortable solution.
Here is an alternative method for removing links from a PDF, if you have Acrobat 9:
- From the Advanced menu, select "Document Processing"
- Choose the "Remove All Links..." option
- Do it