Yes, as Mike very rightly says, it's a good idea to transfer books to the Kindle (or Kindle app) in batches of no more than, say, 20 at a time, and wait for each batch to finish indexing before loading the next batch. You can see if any books are still being indexed by doing a search for a nonsense string. If books are being indexed the search results screen will say "X items currently unindexed" (or something similar).
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