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If you have sync turned on, they will be synced to the new Kindle when you download the book.
The My Clippings.txt file is just an extra copy of the bookmarks, etc., and not related to the copy stored in the books at all. That won't sync; you'd have to copy it yourself, if for some reason you wanted to keep it on the new Kindle. I often delete mine to clear it out. It gets recreated the next time you set a bookmark, or create a highlight or note.
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