Lost all my paid apps after updating to iOS4!  Apps not in backup!!!

I just updated my iPod touch (3 gen) from some OS 3.xxx to iOS4. After 1-2 hours, I got an error message saying that the backup failed. I looked on my iPod touch and saw that all of my apps were deleted except 4 random ones. Thinking that my apps were safe in my backup, I checked in iTunes. My free apps were still there but my 2 paid apps were gone! They were Doodle Jump and Ninja Fruit. Although it's only $2 dollars - I lost my money! Will Apple give my 2 paid apps or money back? I had all my updates done so my apps were iOS4 OK.
One little note. My iPod touch was jailbroken which makes me worried. All I got from Cydia was Pokemon and Themes. Did this contribute to the problem? Yet, a lot of people jailbreak and don't have a problem. But, I am certain that I paid for those 2 apps. I even got physical invoices in the mail.

"What if all my data is actually lost?"
What data? Your contacts, calendars, etc should be synced to your computer, you can just sync it right back.
" What if Apple bills me again?"
For the apps? I gave you a link to Apple's instructions on how to download apps again for free. Follow them.
" I'm afraid to click "OK". =("
Don't know how to help you there.
"I also don't have any music either. "
Your music should be on your computer as well ( in itunes). That is how you got on the ipod in the first place, is it not? Just sync it back to the ipod
" Is the iOS4 update supposed to restore your ipod to initial settings?"
It does not normally do that ( at least in my experience), but you should always make sure that everything is copied to your computer and backed up before you install an update or do a restore.

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