One of the four-and-a-half screenfuls of apps that iTunes deleted from my iPad when I last synced it (over a cable, the old-fashioned way). Now, when I look in iTunes, I can see the deleted apps all re-arranged onto new home screen pages; but none of these apps are on the iPad itself. Amongst other annoyances, this has cost me save states in several games, such as Broken Sword where I was hours into the game.
I am extremely irritated about this. There is no rhyme or reason to the deleted apps that I can see; some of them had pending updates (i.e. the version in iTunes was newer than the version on the iPad), but some didn’t. Some were Universal, some iPad-only, some iPhone-only.