If the case was dismissed a year ago, then Flynn would have been an innocent man who had spent a fortune clearing his name. By letting the case drag on to the point where Mueller's team has been exposed for what they've done so late in the process, they stand a better chance of having the case thrown out along with a judicial finding of prosecutorial misconduct that will allow them to sue the U.S. Department of Justice to recover damages.
Your insight is compelling. It will be interesting to see how this plays out.