OK. Given your description, I think your "un-file-vaulting" failed, and the real problem is that your data isn't where it's supposed to be. It also sounds like your backup drive is in the exact same state, given what you've said.
Disconnect your Backup drive and put it aside. Then, I'd suggest calling Apple. Tell them that the un-FileVaulting failed, and hopefully they'll be able to help you recover...
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--Dave Nanian
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