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Alright, thanks for your help. I've gotten a better understanding of the Fire HD indexing after some experimenting.
1. It seems like indexing doesn't occur until the book is opened (or maybe "priority indexing" occurs when a book is opened for the first time).
2. A first pass occurs which gets all unique words in the book (which populates the autocomplete list) after which later passes get the instances of the words.
3. Results may be listed even though the indexing isn't completed or has been interrupted (Test: I couldn't find a specific phrase near the end of a nearly 2 million word book but I can find results through about 9/10 of the book).
In any case, it may just be the case that the indexer gets really confused with extremely long books and I shouldn't rely on it in the future (I can just search things up using the Calibre reader on my computer instead). At least the status of books being properly recognized by the Fire HD as previously read might have been fixed over the course of all this.
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