Ok, extreme irritation here. I was playing Jetpack Joyride again this evening when it crashed and dumped me out to the iOS main screen (this was on my iPhone, not my iPad). Well, that's happened before; not with the latest release, but it's happened. So, return to the program a bit later, and it's at the main game screen. Ok, that might not be unexpected, what mission was I on, again?
The three missions look familiar: reach 500m w/o collecting coins, play 3 games, collect 5 vehicles. Ok, that's not good. Go to the stash. Still have my (485k) coins and upgraded outfits, jetpacks, and vehicles. Ok, that's good. What about badges? Yep, as I suspected, back to zero. Lost badge #013 before I could record it (Badge of Good Luck, maybe?), plus my other 70-ish badges I'd gotten on this device. Grrr...
Guess I'm going to have to restore from backup, and hope it gets things right.
Update: Well, I lost two badges (079 and 013), but the restore got everything else right. Irritating, but I'll live with it, I guess. Oh, and now I see that I managed not to lose the app I'd bought earlier today on the phone. Yay for things going as they should.