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The indexing system has been vastly improved since the 'old days' when it gave a lot of trouble.
But even so, 3000 books might be too many.
3,000 books in 3,000,000,000 of available storage doesn't sound like: "too much" but you have to remember the 'behind the scenes actions'.
There is another user storage area that you can not see or access -
It holds a number of databases which keep track of things about each book (like notes, highlights, bookmarks, I really don't know all, but anyway, a lot of information).
And that storage area for the databases is much, much, smaller than what you can see.
There is a good chance that you would exceed the limits of that hidden storage with 3,000 books.
Stick with 300 at a time if you can, things are less likely to break with only a few hundred on the device.
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