Upgraded to iTunes 9.2 and iPhone 4 -- all of my third-party apps missing

I'm not exactly sure where the issue came from, but I somehow lost all of my apps as I upgraded to iTunes 9.2 and the iPhone 4 today. But I figured out what happened and *I have the solution*, which I'd like to share...
This occurred on June 24, 2010 (iPhone 4 launch day). The steps I took to upgrade to iTunes 9.2 and iPhone 4 were as such:
1) I did a full sync and backup of my iPhone 3GS with iTunes 9.1.
2) I upgraded iTunes 9.1.x.xx to iTunes 9.2.0.61 (the first version compatible with iPhone 4).
3) I activated my new iPhone 4 and set it up based on my 3GS's back up data.
4) When it was done setting up the iPhone 4, I noticed that all of the native apps and their app data were intact, but I was missing all of my third-party app store apps. Note that all the apps on my 3GS were obviously still intact.
5) I noticed that I had zero apps in the iTunes library (at the top left under "Library"). Thus, with my 3GS plugged in, I right clicked on the iPhone in iTunes under "Devices" and selected "Transfer Purchases". This transferred all of the apps on my 3GS to the iTunes library.
6) I plugged in my iPhone 4, and noticed that on the "Apps" tab under "Devices / iPhone name", the "Sync Apps" box was unchecked. So I checked it, and it gives you a scary message saying that all of the apps in the iTunes Library (which I had just populated in step 5) will overwrite the app data on your iPhone. I didn't have any app data on my iPhone 4, so I clicked "OK". All of the apps transferred from the iTunes Library to my iPhone 4 with all of the app data (game saves, etc) intact.
So that's my solution. I'm sure this must be happening to other people. My main piece of advice is: after upgrading to iTunes 9.2 and syncing your old phone for the last time, make sure you have apps in your App Library and "Sync Apps" is checked. If not, follow the steps above.
This same issue also happened to my friend, but he doesn't have his old iPhone 3GS to restore the app data from. If anyone has any suggestions as to how he can save his app data, please let me know. Thanks.
Craig

Well this won't work for me...
I had all of my apps and music stored in iTunes, I updated to the newest 9.2 iTunes and did a 4.0 update to my iPhone 3G all the while not noticing that EVERYTHING IN iTUNES was GONE. When I got done updating my iPhone it was late so i went to bed... Next day came back to sync everything and thats when I saw it was all gone...
http://support.apple.com/kb/HT1451
did what the link said and NOW I have all my 6K+ MUSIC back but not ONE APP. The App's are completely gone from when you nav. to the location the link says... There isn't a mobile sync folder there...
NOT SURE WHAT TO DO NEXT... Very Frustrated and MAD. I don't want to redownload all my apps manually. TO many to do it that way.

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Well this won't work for me...
I had all of my apps and music stored in iTunes, I updated to the newest 9.2 iTunes and did a 4.0 update to my iPhone 3G all the while not noticing that EVERYTHING IN iTUNES was GONE. When I got done updating my iPhone it was late so i went to bed... Next day came back to sync everything and thats when I saw it was all gone...
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did what the link said and NOW I have all my 6K+ MUSIC back but not ONE APP. The App's are completely gone from when you nav. to the location the link says... There isn't a mobile sync folder there...
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