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Found this thread via google while looking for a way to delete my vocabulary builder. The SQLite Manager addon for firefox mentioned above worked nicely (You can also put the SQL commands in there and execute them). However afterwards you have to compress the database, because even if you delete the contents of WORDS and LOOKUPS, they apparently are still in there somewhere. After deletion and compression the vocabulary builder is finally empty.
Btw, I've tried to simply delete the database from my kindle because I thought it would create a new one when I look up a new word, but no, it did not. When you simply delete vocab.db from your kindle, the vocabulary builder won't work any more (at least if you keep your device offline. Otherwise it will download the db from the Amazon servers if I'm not mistaken).
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