When the Kindle Paperwhite is synced with the Amazon account, it never syncs beyond 1023 (
2^10 - 1) books.
How do you access books beyond the 1023rd book in an Amazon account on a Kindle Paperwhite?
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This sounds like a limitation of the software, so you probably won't be able to get around it from the device.
First, I recommend reporting this as a bug to Amazon. Don't expect them to fix it right away or anything, but it's always good to let the devs know when something doesn't behave as you as a user want. ;)
If your final goal is to get all your books to the Kindle somehow, the solution would be to download them from Amazon ("Your Content and Devices") and sideload them over the USB cable. (It's good to download the files as backups anyway and de-DRM them while you do that, IMO, but that's a different topic...)
EDIT - how to report a bug: I forgot that Amazon is one of those "don't bother us dirty mortal!" companies. The only way to report a Kindle bug I found is to use the form at /gp/help/support/contact-us (choose "Devices" from the buttons above) - and whow, that is one very well-buried page!