I knew about the “transfer purchases” option when doing a right click on the device but since all the Apps when synchronizing back and forth from the iPad, iPone and iTunes automatically, I was careful about that feature.
As you will see, the problem was related to the fact that I had set up iTunes to “manually manage music and videos”.
So, I went ahead and first transferred all the purchases made on the iPad. I immediately got the warning that “All existing songs, movies and TV shows will be removed from the iPad”. Purchased books were transferred to iTunes but songs and movies were completely removed from the iPad… By the way, PDFs and manually added epub titles I had made with Calibre were also removed from iBooks and they had not been transferred to iTunes.
I went to the Music tab in iTunes and selected “Sync Music” and “Selected playlist, artist and genres”, made my selections and sync back music to the iPad.
From that point, I was not able to copy songs from iTunes’ playlists directly to the iPad as I was previously doing. Selections needed to be made on the “Music” Tab in iTunes. The same with movies: I cannot drag an MP4 movie with Explorer directly to iPad; I need to drag it to iTunes’ main Library to populate it and then, form iPad’s “Movies” tab, check “Sync Movies” and make my specific selections.
The same steps needed to be done on iPhone. All Books were then copied to the iPhone.
Next, I purchased a new book directly on the iPad. When I synchronized it to iTunes, that new purchase was automatically transferred. Then, synchronizing the iPhone got me that book on it.
From there, when I stop reading a book on the iPad and then go to the iPhone and open that book, it opens exactly where I left it on the iPad. This is done over the air. I am not sure if it uses MobileMe or not, but it works.
This setup is a lot more functional that what I had before, not to mention that iBooks’ purchases are now being backed up in iTunes.