Will bookmarks, highlights and notes disappear after "personal" editing?

I have to read many .epub classical books (almost all public domain) on iBook. Those books are not necessarily from iBookStore. I make highlights, notes, etc.
My situation is that the formats/styles and typos of those classical .epub make me extremely uncomfortable.
So I am planning to edit those errors whenever I find them on my Mac.
Here is the workflow:
Read on iBook ——> highlights ——> see errors ——> export .epub to editing tools on Mac ——> edit ——> export to iBook ——> read
My only question is will all my bookmarks, highlights and notes disappear when I edit the epub?
Does anyone know where/how iBook records/store the highlights and bookmarks? In .plist or something else? Since If I know where all my annotations are, I couse easily preserve them when I am editing the epub.
This is a very very big problem of mine. Please help me.

Connect iPad with iTunes Mac and copy the book to Mac. Then import it into Sigil (an open-source epub editor) http://code.google.com/p/sigil/.
In Sigil, edit whatever part I need. Then export to iTunes again and sync with iPad connected.
After this, the book no longer belong to the iCloud, but treated as ordinary epub imported into iPad.

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Will bookmarks, highlights and notes disappear after "personal" editing?

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