I had the same issue with my brand new Iphone and my Macbook Pro ICal. In short, after hours on the phone and at the Genius Bar, my calendar is back on the computer (thanks to a lucky back up I had), partially on the Cloud (Choosing to ignore all my Blue dates while copying three other colors) and nowhere to be found on the phone.
I've tried turning off all cloud computing and syncing through ITunes. It says it's syncing, but it does not.
I've tried turning all Cloud computing on and letting it sync that way. Nothing has changed.
I wish I could tell you how we finally got the "upgrading" message to stop, but I don't recall what folder the Phone Support took me into or what file we ultimately had to trash. I do recall it was going to erase whatever was left in my calendar.
In short, I've learned that IOS is not interested in interacting with OSX Lion. And beware the OSX Mavericks upgrade, because that disables most of the few remaining conveniences that do exist between the two.
At this point, I have one more week to either keep or return the IPhone and if I don't get this thing
solved by Monday.... It's back to Android for me. Hard to believe my HTC Evo did a better job or relating to my Macbook Pro than Apple's own phone.