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I wonder if by having so many books on your Kindle, that this caused it to overrun storage somewhere. This type of aberrant behavior is usually a software bug due to a developer not realizing that a user would surpass some arbitrarily huge limit the developer had set. Once memory/storage gets overrun, it can get corrupted, so the Kindle might think it needs to start indexing all over again. And the second attempt will probably end as badly as the first.
I assume you are using Calibre, since most here do. If not, definitely look into it as your primary ebook organization. Then only put a few books on your Kindle rather than thousands. Swap a reasonable amount of books in and out as you finish some and need others to choose from. I generally keep one to two dozen "potential next reads" on my Kindle - so I have a choice, but not an overwhelming one. Calibre holds all the rest to be swapped in later, as the need arises. A Kindle would be very poor at navigating 2000 books, the user interface for that is just too poor IMHO. I believe the Kindle indexes every word in every book. Ugh - that's quite a task for such a low powered device (processor/ram) to manage. Plus, trying to index so much all at once (like yours appears to be doing now) will run down the battery quickly. If it dies part way through indexing, that's another potential pathway to corruption.
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