I have no idea how you might retrieve information already lost, but here's what you need to do going forward... You need to switch to Calibre on your PC to manage your books collection: don't use itunes. You can manage the metadata there, edit and change it to your heart's content and that will transfer to your phone. On your iPhone, almost any app other than iBooks would be good. I'd recommend Marvin and Hyphenreader, both of which manage notes well, and will sync between devices if you had more than one iOS device. There's Calibre companion for iOS but I find it a bit clumsy, I prefer to use my computer's collection to download books from.
Calibre is a really powerful software program and it has its own forum here on mobileread.
https://www.mobileread.com/forums/fo...play.php?f=166
If you have been buying books from Apple, you'll have to contend with DRM, those books wont be able to be opened by anything other than iBooks, unless you can find a way to remove the DRM... and I cant help on that matter at all.