Stay with me here....
Assume Hillary is actually right (yeah I know). Comey was so disturbed by his decision several months ago that the first letter 2 weeks ago was sent to ease his conscience for letting her off the hook and giving her great momentum. Also, to placate his fuming FBI pals.
He knew the damage was done with the first letter and the letter written two days before the election was a triangulating political move that had very little affect on the outcome.
Remember, there were numerous leaks from the FBI after he initially let her off but nothing after the second time. It seemed like a coordinated FBI plan agreed to by Comey and his colleagues.