It doesn’t matter if you link a Goodreads account or not. Sync is one way (from Kindle platform to Goodreads).
Tellingly, these highlights an notes never synched to your account but were confined to this particular device, else the re-download would have restored them. I suspect data corruption to the sidecar files containing them is a strong possibility. Sync could fail as a result, and random highlighting could result as it tries to make sense of what is in the corrupt file.
The other theory involves a cat playing with your Kindle.
My reasoning is somewhat motivated but I don’t think there’s evidence of privacy breach.
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