Originally Posted by Japes
This is exactly why it's not a good idea to load hundreds of books onto your Kindle at the one time.
If you do it in small batches (say 20-30) and check to make sure they are indexing ok inbetween, then at least you've only got a small number of books from the last batch to delete and help you identify the problem one.
That's probably your answer. Delete them all, and start reloading them in small batches until the indexing gets stuck again, then it's easier to find the one that's causing the issue.