Upgrading to iOS4 - DO NOT Sync your Apps yet!

Hey all,
Unless I'm missing something, I'm anticipating a major annihilation of our purchased apps! I'm on a 3G, I have a bunch of purchased apps, went through the upgrade process today, did exactly what iTunes told me, watched the little bars for over an hour when it said it was backing up, restoring, etc. and when I started fiddling around with the new app folders feature on my device I figured it would be quicker to arrange everything visually in iTunes. So I went to the Apps tab and my phone was visible but the app pages were greyed out and I couldn't move them.
Hmmmmmmmm.
So, I clicked the "Sync Apps" button and got a pop-up message that gave me a little warning in a polite but hidden agenda Apple tone to the effect of "You think you should click this button, we're making it seem as though it will be okay, but what you don't realize is that because it's an OS release day and we haven't sorted things out yet, you're about to be screwed.....maybe, but probably, and only we really know, we think, cause we change everything."
Now, I clicked "Sync Applications" and nothing on the phone started happening.....however, the "Sync" button on the lower right corner was available, which I'm assuming is the real trigger that one needs to pull to make this happen. So, I DID NOT push that button, however, my app window panes were all rearranged graphically and I had the option to move things around.
Here's the kicker:
Most of my purchased apps were GONE. Only the stock apps remained and some of the purchased content was there but at least 70% of my paid apps were no longer "on the device" in the layout. I checked the Apps tab in iTunes preferences to get that info available in my sidebar and NOTHING showed up at all. So, in updating iTunes, my little Apps library disappeared as well.
Back to the actual Phone....everything is still intact, remember I never hit the bottom-right "Sync" button, but I am left to believe that we have a time bomb on our hands here. People are going to update, hit these "Syncs" and lose their material!
Anybody know what is up here? Did I do something wrong?

Fixed it......
The problem was my Apps library in iTunes was not populated with the apps on my phone after the update of iTunes and iOS4. Therefore, that is why I "lost" them visually. Now, had I gone and hit "Apply" I would have been screwed, since nothing was in my iTunes App library.....Sneaky.....
In iTunes, File>"Transfer Purchases from iPhone"
This populates the iTunes App library with the apps on your device. It will take a few minutes, but all of the apps will now show up when you go back and try to sync the iPhone.
Screenshot of Success!
http://i55.photobucket.com/albums/g134/leonardrock/Screenshot3.png
Nice, I'm not stupid.
Thanks for the chime-ins everybody!

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