Sync Error/Apps Erased

Tonight while syncing my iPhone I attempted to sync a couple podcasts. Once I checked the ones I wanted and hit apply everything went wacky. First off I got a sync error -50 and then my Apps were completely erased from my phone. I had never touched the Apps tab in iTunes. Also, somehow all the data stored in my apps was deleted too. So all the notes I had in Awesome Note were gone and the gas tracking I did in AccuFuel was gone, etc.
Is there anyway to get that information back? I've re-synced my phone now without problems after adding all the apps again through iTunes, but the podcasts were unchecked again and I'm loathe to try to sync them again. Is this a known issue when trying to sync Podcasts?

Contact Apple. They may re-authorize download of apps you've purchased.
Next time, pay attention to the warning messages telling you you might lose everything instead of just ignoring them.
Honestly, they did NOT put the warnings there just to annoy you. They actually mean something.

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