AFAIK, the clipping limit of many commercial (text)books is usually 10% of the book's content. Once you've reached this limit, the Kindle will no longer save text in My Clippings.txt on the device or the PC.
You can test whether a particular book has a clipping limit by checking for the presence of a
exth 401 record with
Java Mobi Metadata Editor. If you find one with a value of less of than {100}, the book has a clipping limit.