Also, be sure you ALWAYS allow the game time to save appropriately before shutting down the game or your Xbox (a lot of people rush this and wind up corrupting the save file in the process).
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I do back up my files before updating and I always back right out of the game before turning off my Xbox.
Unfortunately, saving to a USB after you've already accepted the update once is like trying to close the barn door after all the horses have already fled. Backing up prior to the update gives you an untouched file to copy back onto the hard drive if the one on the hard drive gets damaged by the update process, but if the files have become damaged during the update process, the damage is done and there is no way that I'm aware of that it can be undone.