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Highlights and notes deleted

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About half of the highlights or notes I've made have been deleted. If a document still has any highlighting, it seems to have it all, but half the documents are now just blank. Is there any way to recover all the work I did and notes I made? I created a backup but it failed three times before it worked and even though it's from before the highlights had originally disappeared, they're still gone. I read about other people's problems and will say that none of the files/pdfs have been moved and the folder structure is completely identical.

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