As far as I understand (and I have no personal experience - just snippets I remember reading online) once the limit is reached, I'm not sure there is anything you can really do to overcome that. Other people have reported that going back and deleting highlights
does not free up room for new highlights and that somehow the Kindle remembers that the clipping limit has been reached and nothing else from the book will be added into your My Clippings file.
If I ran into this problem myself and wanted a way of adding new notes/highlights which could be extracted for say copying or printing on a PC, I would at least try sharing the notes using the social networking feature but whether the Kindle is smart enough to turn this off as well once the clipping limit is reached I don't know:
http://www.kinworm.com/2010/12/easy-...-all-your.html
Have you resolved it yourself? What happened when deleting the .MBP file? Be good to know for anyone else with the same problem.