if you unformat, are the correct links there? – this is often due to a corruption/deletion of part of the field, or sometimes using an unusual character in the prefix or suffix field of an edited citation (but that was an old version’s bug). Endnote tech support does have tools to shift them back as noted in the above link.
If the unformatted ones are in the right place, I would run the clean up document steps on that section in a new file and put the unformatted text back in, and format it there. http://endnote.com/kb/81143
support pages provides this contact info for Australia & New Zealand