Or it might be a case where Kelly was "charged up," that is prosecutors threw everything in that the could, hoping the magnitude and volume of the charges against him would make him enter a plea agreement on the most serious charges.
Since it now seems as if this is headed for trial, prosecutors may have simply thrown out all the extra, and harder to prove charges, and are now prepared to try him on what they felt were the serious (and most provable) charges all along.
...I'm not an attorney, but I did stay in a Holiday Inn recently.