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First you should check 'My Clippings.txt'. It will have a copy of all annotations you've made, unless you deleted it at some point.
If you side-loaded everything (did not use Send To Kindle service to store your documents in cloud) then there isn't any cloud backup for your notes and highlights.
If you did use Send To Kindle, then you have cloud backup for both the documents and their annotations. At any time, you can register a Kindle app (e.g. on a cheap Android tablet or iOS device) and you can download the document to it and Export notes for that document as an email attachment. The Export feature on newer Kindles does not work with 'personal documents', however. I believe newer Fire tablets support Export as well but I don't have one to verify if it works with personal documents.
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