PDF in Preview does not reflect in iBook

I am using Preview 7.0 to open and edit PDF. Typically, I use highlight, underline, add notes etc, all within the Preview app in Mac Pro 15 Retina OS 10.9.4.
I am also using iBook 1.0.1, when I add the "edited" PDF to iBook (and later sync via iTune to my iPad), and open in directly inside iBook (on my Mac or on my iPad), all the "edited" portion did not show.
Is this the intended outcome where iBook does not accept all the changes I made to the PDF? Or I did not do the right thing?

There is no mail option under the share icon - does it only show up if I change Mail Prefernces to show Mail as the default - seems very silly...
Why would I need to re-start my MAC - I havent changed anything yet?

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