Clippings aren't unlimited. If you clip too much, you'll see a notice in your My Clippings.txt file to the effect that your limit has been exceeded instead of the highlight or clip you made. You can still highlight within the book, but those clippings over the limit won't be copied to your My Clippings.txt file. The clipping limit is set in the header of the e-book file and interestingly (to me, anyway), when set, the clipping limit is enforced even on DRM-free files.
It's not really documented anywhere, but 10% of the book seems to be the general limit. It is something that publishers can specify; O'Reilly completely removed the clipping limit from their Kindle books
http://toc.oreilly.com/2009/10/kindl...lly-books.html