Apple released iBooks 3 this week, which lets you store your eBooks in iCloud and includes a continuous scrolling feature.
When you update to the new version of the software, most of your notes and highlights will be preserved in your text of your eBooks, but some will require a little digging to find. For example, if a book has been edited or the publisher has moved anything around in the layout, then your highlights may have moved to a new location within the file. Most of these highlights have ended up in the “Old Notes” section.
Check it out: “If the passage you have highlighted has not been edited, but has been moved to a different section within the same chapter, iBooks may be unable to display the highlight on the page, but it can still be found in the Notes View. Check at the end of the chapter in an ‘Old Notes’ section.”
Bookmarks will be preserved if the page that you bookmarked hasn’t moved. If the page you bookmarked has moved then the bookmark will be discarded. And if it has been edited, then iBooks will estimate where the bookmark belongs.