Here is a kindle highlights fetcher (with source code):
https://rubygems.org/gems/kindle-highlights
https://github.com/speric/kindle-highlights
It may have some code snippets to guide you in your "missing highlights" recovery efforts.
One note of interest regarding this tool:
Quote:
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Amazon will sometimes issue a CAPTCHA challenge when logging in to your Kindle account. If this happens when the gem attempts to log in to your Kindle account to retrieve your book list or highlights, you'll get a KindleHighlights::Client::CaptchaError ... There's no way to programmatically resolve this situation. The best solution I've found is to open a browser, visit the URL that the gem returns, log in to your Kindle account, and click around a bit. Then log out of your Kindle account and re-attempt to fetch your highlights via this gem.
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