Where did my apps go after upgrade of iPhone 4 to OS 5?

After going through the process of backing everything up and upgrading the software, my apps are gone.  When I go into the app store, the apps i had show install not a price or free, so there is something clearly indicating i had these apps.,  However the data associated with them is gone if i download them
Is this what i should have expected?  Is there a way to get the apps and their data back?
Thanks

I found that the iPhone appeared to have finished syncing, but in fact the apps were still being copied back to the phone from iTunes. If you wait a while (with the phone connected to your computer), you may find that they just keep appearing. Mine took about 30 mins.

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