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You won't overload your Kindle -- I think the worst that can happen is one of them jams the indexer and you have to go through tons of books to find out which to delete. For that reason, you might want to do it in small batches, and confirm that the Kindle finds all those books before adding more.
I mean, I assume that by indexing taking a long time, you mean this question to refer to the search indexing - not just the shows-up-onscreen indexing. Right?
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