Purchased app on iPhone - disappeared when synced with itunes

I purchased an app on my phone a couple weeks ago. Today I synced with iTunes on my PC and the app disappeared from my phone and does not appear in the list of apps in iTunes. "Check for available downloads" in iTunes said that I had no available downloads. The purchase of the app did show up in my purchase history, but that seemed to be the only place.
I was able to get the app back by attempting to purchase it again, at which point iTunes allowed me to download it again for free. However, all of the application data is still gone. And since I synced more than once in this process, the initial iPhone backup (which should have contained all that was lost) has now been overwritten.
This has happened to me several times before, but this is the first time where the application data has been important.
Any ideas as to what went wrong?
Is there any hope for me to recover my application data at this point?
Any way for me to prevent this happening again? (short of never syncing...)

I doubt very much that you can recover the data at this point. The safe way to do things (I found for me at least) is download apps initially via iTunes instead of your phone, then mark them for syncing and do the normal sync. I purchased all of my apps this way and sync several times a week with no problem. I also do all the app updates thru iTunes.

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