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I lost my original hard drive, and I have some books (in ePub format, I believe) on my iPad 3 that have bookmarks and highlighted stuff which I'd like to preserve.

Is there any way to get that info back to my iTunes? I did not purchase them through iBooks or iTunes.

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If you didn't buy the books via iTunes or iBooks, the files are preserved only in your backups, and as far as I'm aware, there isn't a supported way to recover them back to iTunes.

If you were to jailbreak the device, you could go on a fishing expedition, but I doubt what you're looking for is possible.

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they were not purchases –  devoured elysium Jun 1 '12 at 3:28
    
I've rewritten my answer based on this new information, and updated your question to reflect this. –  user3463 Jun 1 '12 at 22:01
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