There's an app called
Kindle Mate which allows you to backup your clippings and words from vocabulary builder. Additionaly, you can delete all words at once and update status to Kindle. I did it, I had more than 2000 words*, and syncing did not brought them back...
* btw: vocabulary builder, on kindle paperwhte 2, does not display number of searched words bigger than 2000, but all underlined words actually were there, so i had like 2200-2300 words, and kindle was really sluggish because of this.