I'm afraid to say that in my case the re-indexing of my books (2000) signaled the deteroriration of my Kindle. It was the sign of it's getting unstable.
I would let it charge
while that indexing is done, as it takes a lot of batterylife (which isn't properly indicated on the Kindle) and hope for the best. Don't do anything on it during that time.
To see if it is still indexing, try to type a random search like ' xdaqz' or some other; it will show the number of books to be indexed.
This being said; I hope it will work out. Positive thing about Amazon customer service is that they're quick and friendly.
And if you've got a really big problem; it is best to phone, not to email. And if you think it could be better; phone twice; to get another person on the line.
BTW. Did you load all your books in one go on the Kindle? I've experienced that it's best to do in it batches of 2/300, let it charge while indexing (can take some hours though) and give it a rest.