I lost all my app data!

I was installing an app on my perfectly functioning iPhone, and it caused my iPhone to freeze.
I had to perform a complete restore. But I had backed up my iPhone in iTunes, so I wasn't that upset about it.
I went to the Apple Store, because I could not do anything to get it to unfreeze. They helped me. And did the restore for me.
We then applied my most recent backup and I got everything back in order.
Well, everything, that is, but my app data. Gone forever. Every single app: pennies, iXpensit, my 3 fuel gauge apps. OmniFocus, ToDo. All gone.
I am so happy about Evernote. Because it syncs to the web and to a desktop app. So I have all that information.
I had worked really hard to be organized. Some of these apps were godsends to my life. It makes me sick that I lost all that data.
What is the point of using them, if the data can be wiped in a second.
My iPhone and your iPhone will crash at some point. Somewhere down the line we will all probably have to do a restore on it.
So why use these fantastic apps and put all that time and energy into them, if it can all go on a moment's notice?
The apps are the greatest. I love them. I still love them.
But this backup issue is essential.
Anyone have any idea about how to protect myself with backing up these kinds of apps?
I am really upset about this.
Thanks.

So did I, for the third time. I have previously had two "Lost Apps" crashes, resulting in complete factory resetting. After reading about succesful resetting by deauthorizing/reauthorizing the phone in itunes, I became a bit brave, and wanted to download some new applications...
This time, iTunes did not want to talk to my iPhone this morning, claiming that the iPhone returned wrong response. I then did a power reset, and after that it was just the White Apple Logo of Death.
To speed up the factory resetting and reload, I deleted about half of the apps in iTunes (since the large number may be a reason for infinite loops in iPhone startup as reported elsewhere).
So now we just have to wait for some updated software that makes us start trusting the device with our data again. For the moment I am only using apps where I can have a synced backup somewhere else (NOT relying on the itunes Restore function).

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