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I've had this error occur with a Kobo. It's caused by, well, a communication problem. You likely have an issue with the cable, such as quality issues, bending, unstable power supply, etc.
When this happens to a Kobo it messes up the database on the Kobo (and that's not going to repair itself). That can be restored by signing out and signing it to Kobo, but that will temporarily lose Collections and stuff like Annotations, etc. Calibre can backup a Kobo database.
I don't know if there's a Kindle equivalent. I hope so.
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