Data lost with 3.1 update

I dutifully downloaded 3.1 and had done a software update which updated iTunes to 9 on my MBP 2.5GHz/250GB-5400/4GB 667DDR2 RAM. When I synced my 32GB 3GS iPhone, ALL of my apps were deleted from the iPhone, then all 96 of them were reinstalled, including a bunch I had taken off the iPhone, and reinstalled the in ALPHABETICAL ORDER (who in the heck installs their apps alphabetically?)! Worse, I am "New user" on all my apps, all my lists are gone from my list apps, dates gone from countdown and calendar apps, word lists from dictionaries, maps I had downloaded from Topo Maps, scores for all my games are gone!....AGHHH! I was at work a few days ago, I went to look up a drug interaction on Epocrates, they had never heard of me, and requested that create a new account etc. Sorrrrryyyy I am just a litttttle too busy right now! So I looked it up the old-fashioned way. iTunes 9 does make it infinitely easier to rearrange the apps, so I worked that problem out pretty easily, thanks to the new iTunes.
Does anyone know what happened? Am I a victim of the "5th finger" phenomenon, where you inadvertently hit a key with your little finger and all of a sudden weird things start happening? Did I miss a really important alert box that warned me that my digital life was about to change? Right now American Heritage Dictionary 4th ED is downloading, which takes over an hour on my DSL, but I already have it. AND there is an alert that I have an app to update, and it's the AH Dictionary! But when I click on the icon, it says I purchased it but haven't downloaded it, go the the iTunes store and click on available downloads--but I HAVE downloaded it, and it is downloading again.
Fortunately, I have not suffered the fate of many as witnessed on the Apple Support Discussions or MacWorld forum, but I am curious if anyone else has had my experience? I am perfectly willing to admit that I may have missed an alert box, but I don't know if that is what happened, of if it was 5th finger episode, or what.
Thanks. Any input/feedback is appreciated.

Wow this sounds suspiciously like you didn't restore from a backup.

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