I think I finally made this go away. The only thing extra that I did was to "Unhide" an app that I had hidden in the iTunes store. The interface is really obscure, hidden in the iTunes store.
If you go to the "Purchased" link on the iTunes home page (NOT the "Purchased" item in the sidebar -- these show two completely different lists/user interfaces, despite being named the same!) you will see all the items you've ever purchased--except that when you hover over one of these items a little 'x' icon will be overlaid on it. If you click it, the item goes into a "hidden" list and will no longer show up here.
To see any items you might have hidden, go to your Account page (using the Account link on the iTunes home page, or selecting Account from the drop-down menu that appears when you click your Apple ID in the upper left corner). If you have any hidden purchases, you will see an entry in the "iTunes in the Cloud" section reading "Hidden Purchases:", with a "Manage" link. Clicking on Manage shows all your hidden purchases, subdivided into tabs for Music, Movies, etc. Tab through them all and if there are hidden items, click the Unhide All button in the bottom right corner. Also note that the Apps tab is further subdivided into iPhone and iPad sections.
I don't know for sure if this was the key to getting things to work, but I do know that after doing this the problem went away for me. After unhiding the app, I did another Transfer Purchases and this time a completely different app - in fact, Garage Band, which I hadn't hidden, transferred from the phone to my Mac.
I started the iOS update again, and the message did not appear. I think what might have happened was that the app I had hidden had, for some reason, never actually been transferred from the phone to the Mac at the time I hid it. I don't know where Garage Band fit into things... maybe there was just some corrupted DB entry that got cleared when I unhid everything... hard tellin', not knowin', as my grandpappy would have said.
Anyway, HTH. PS, I have to say, I agree with all the posters who wonder why syncing doesn't count as a "transfer"...