Why did iTunes confuse my existing iPad and my new iPad?

I synced my new iPad to my Mac and specified that I didn't want music to sync. That appeared to work ok. I then synched my existing iPod Touch to the the mac and iTunes deleted music. I ultimately reloaded it all but now I'm concerned about syncing again. How can I prevent this confusion from happening? I also just upgrade iTunes but haven't yet installed IOS5 on the other devices.

I guess I should have included a little more info:
1. I only have 1 appleID
2. I only have 1 apple device (the one iphone, nothing else)
3. I only sync on one computer (VERY annoying you cant use more than 1!!)
4. I never have any other problems during syncing and don't change any settings
5. I downloaded the app again so it is back.
I am not asking how to get the app back, I just want to know WHY itunes deleted this app. This is the second or 3rd time it has happened and it is really annoying.
I also would like to get my files back. So again, I'd like to know why itunes deleted the app and if it deleted my files as well.
The most important part of this is to find out WHY this happened so that it wont happen again. It seems to be a pretty simple operation: Plug the iphone in, itunes opens and does a sync. It almost always works perfectly, I never change any settings. Yet every once in a while it deletes a newly installed app so obviously something is wrong. If I can find out what I did wrong, then I can avoid it in the future.
Thanks!
Scott

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